1 fx 1.10 -*- mode: indented-text; fill-column: 78;-*-
2
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3 ccb 1.200.2.14 Summary of significant changes to CCP4 at version 6.1.3 ("No name")
4 ---------------------------------------------------------------------------
5
6 * Building etc.:
7 * gnu compiler 4.4 compliant
8 * supports Snow Leopard
9
10 * Program changes:
11 * IPMOSFLM: updated to 7.0.5
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12 fr45 1.200.2.19 * REFMAC: updated to 5.5.0109
13 * MOLREP: updated to 10.2.35
14 * SFCHECK: updated to 7.3.16
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15 ccb 1.200.2.18 * POINTLESS: updated to 1.4.2
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16 fr45 1.200.2.19 * CTRUNCATE: updated to 1.0.10
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17 ccb 1.200.2.14
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18 ccb 1.200.2.16 * Library changes:
19 * MMDB: update to 1.21
20
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21 ccb 1.200.2.14 * Graphical User Interface:
22 * IMOSFLM: updated to 1.03
23
24 * Bugs fixed:
25
26 * Known issues:
27 * 3488: IMOSFLM: cannot launch batch jobs from interface
28 * 3630: SCALEPACK2MTZ: does not read symmetry from input file
29 * 3894: DBhandles not python 3.0 compliant
30
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31 ccb 1.200.2.12 Summary of significant changes to CCP4 at version 6.1.2 ("Ingleborough")
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32 ccb 1.200.2.10 ---------------------------------------------------------------------------
|
33 ccb 1.200.2.9
34 * Building etc.:
35 * ccp4.setup-dist renamed ccp4.setup-csh
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36 ccb 1.200.2.12 * ccp4i, crank, imosflm launchers copied to bin directory during
37 installation
38 * csh no longer used during installation, all steps use sh
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39 ccb 1.200.2.9
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40 ccb 1.200.2.12 * Program changes:
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41 ccb 1.200.2.10 * POINTLESS: updated to 1.3.9
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42 nds65 1.200.2.13 * SCALA: updated to 3.3.15
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43 ccb 1.200.2.12 * REFMAC5: updated to 5.5.0098. PHOUT added for building of MR solutions
44 with BUCCANEER
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45 nds65 1.200.2.13 * MOLREP: updated to 10.2.31
46 * SFCHECK: updated to 7.3.13
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47 nds65 1.200.2.11 * SIGMAA: new version from Ian Tickle
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48 nds65 1.200.2.13 * OASIS: minor update
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49 ccb 1.200.2.10
50 * Graphical User Interface:
51 * CRUNCH2: new interface for experimental phasing program
52 * CRANK: update to 1.3
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53 ccb 1.200.2.12 * database back end off by default
54
55 * Bugs fixed:
56 * 3596: IMOSFLM: requires project directory to exist, fails otherwise
57 * 3689: POINTLESS loop variable overflow
58 * 3690: REFMAC5 interface not backwardly compatible
59 * 3713: REFMAC5 interface amplitude based twin refinement
60 * 3722: CTRUNCATE in import scaled task
61 * 3790: MOLREP multi-copy search failure
62 * 3797: all_load shared library builds under newer linux ld
63 * 3816: TLSANL anisotropic Us
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64 nds65 1.200.2.13 * various uninitialised variables caught
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65 ccb 1.200.2.12
66 * Known issues:
67 * 3488: IMOSFLM: cannot launch batch jobs from interface
68 * 3630: SCALEPACK2MTZ: does not read symmetry from input file
69 * 3894: DBhandles not python 3.0 compliant
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70 ccb 1.200.2.9
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71 ccb 1.200.2.7 Summary of significant changes to CCP4 at version 6.1.1 ("The New Inn")
|
72 ccb 1.200.2.6 ---------------------------------------------------------------------------
73
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74 ccb 1.200.2.7 * Building etc.:
75 * intel 11: mostly supported
76
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77 ccb 1.200.2.6 * Program changes:
78 * PDB_EXTRACT: updated to 3.004
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79 nds65 1.200.2.8 * REFMAC5: updated to 5.5.0072
|
80 ccb 1.200.2.7 * POINTLESS: updated to 1.3.1
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81 nds65 1.200.2.8 * MOLREP: updated to 10.2.23
82 * SFCHECK: updated to 7.3.10
83 * CHAINSAW: accepts fasta alignment files
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84 ccb 1.200.2.7
85 * Library changes:
86 * MMDB: update to 1.19
87 * monomer dictionaries: various updates, including CYS-MPR
88
89 * Updated interfaces:
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90 nds65 1.200.2.8 * REFMAC5: better integration of SAD refinement
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91 ccb 1.200.2.7 * BP3: interface added
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92 nds65 1.200.2.8 * TRUNCATE: CTRUNCATE options added
93 * DTREK2MTZ: CTRUNCATE now the default for intensity to SF conversion
94 * SCALEPACK2MTZ: CTRUNCATE now the default for intensity to SF conversion
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95 ccb 1.200.2.6
96 * Bugs fixed:
97 * 3628: ccp4i import task
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98 ccb 1.200.2.7 * 3592: SFTOOLS interface
99 * 3619: REFMAC5 interface ignoring external file
100 * 3655: CHAINSAW not deleting CISPEP records from PDB
101 * 3656: PISA writing to $CCP4/share/pisa directory
102 * 3558: CAD segv
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103 ccb 1.200.2.6
104 * Known issues:
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105 ccb 1.200.2.7 * 3488: IMOSFLM: cannot launch batch jobs from interface
106 * 3596: IMOSFLM: requires project directory to exist, fails otherwise
107 * 3630: SCALEPACK2MTZ: does not read symmetry from input file
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108 ccb 1.200.2.6
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109 ccb 1.188 Summary of significant changes to CCP4 at version 6.1 ("Holy Trinity Church")
|
110 pjx 1.167 ---------------------------------------------------------------------------
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111 pjx 1.148
112 * Building etc.:
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113 ccb 1.199 * Refmac5.4+ requires a Fortran90 compiler, as do Molrep 10 and Sfcheck
114 7.3+. Configure tests for this, and disables refmac, molrep and sfcheck
115 builds if not found (e.g. if compiler is g77).
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116 pjx 1.166 * ccp4.setup: the environment variable GFORTRAN_UNBUFFERED_ALL is
117 explicitly set to "Y" in the distributed setup files, to ensure that
118 the log file output from gfortran-compiled programs is written in
119 the correct sequence. This may incur a performance penalty however.
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120 ccb 1.180 * POINTLESS, RAPPER, PISA optionally configured and built with core.
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121 pjx 1.148
122 * Program changes:
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123 pjx 1.173 * AREAIMOL: uses a new "spiral distribution" to divide up the surfaces
124 of the expanded Van der Waals atoms, which gives significant
125 improvements to the accuracy and stability of the accessible surface
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126 pjx 1.176 area calculations - see the program documentation (Ian Tickle).
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127 mdw 1.156 * CAVENV: program now uses symmetry mates of input molecule unless
128 SYMM OFF set. Gives protein and solvent volumes within map limits.
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129 nds65 1.200.2.5 * CRANK: updated to version 1.2.0. Greatly enhanced (Raj Pannu)
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130 ccb 1.200.2.3 * IMOSFLM: update imosflm to 1.0.0
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131 pjx 1.162 * LOGGRAPH: is now able to give a basic view of the XMGR-style
132 normplot and correlplot output from SCALA, for systems where xmgr(ace)
133 is unavailable.
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134 ccb 1.200.2.1 * MOLREP: updated to version 10.2.12.
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135 ccb 1.199 * MOSFLM: updated to version 7.0.4.
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136 nds65 1.183 * OASIS: updated to OASIS-2006.
137 * PDBCUR: new option to delete ANISOU records.
138 * PDB_EXTRACT: updated to version 3.0 (since August 2007)
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139 pjx 1.164 * PDBSET: estimated molecular weight based on the sequence of residues
140 is automatically calculated when the SEQUENCE keyword is specified.
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141 ccb 1.198 * PHASER: updated to 2.1.4. This version covers MR, SAD and combined MR and SAD.
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142 ccb 1.200.2.3 * REFMAC5: updated to version 5.5.0066. This adds twinned and anomalous
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143 ccb 1.198 refinement (Garib Murshudov, Raj Pannu, Pavol Skubak).
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144 ccb 1.200.2.3 * SCALA: updated to version 3.3.9
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145 ccb 1.200.2.1 * SFCHECK: updated to version 7.3.7.
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146 pjx 1.148
147 * Library changes:
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148 nds65 1.200.2.5 * Addition of a new "Diffraction Image" library which also comes with 4 small
149 jiffies installed in bin - diffdump, printpeaks, automask and diff2jpeg.
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150 ccb 1.189 * Monomer dictionary updated to 4.13
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151 pjx 1.148
152 * New programs:
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153 ccb 1.188 * AFRO: multivariate substructure factor amplitude estimation for SAD/MAD
154 (Raj Pannu)
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155 pjx 1.177 * BAUBLES/SMARTIE: new program for re-rendering CCP4 log files with
156 HTML markup (Peter Briggs & Kevin Cowtan).
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157 ccb 1.195 * BALBES: automated molecular replacement (Fei Long, Garib Murshudov,
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158 nds65 1.200.2.5 Alexei Vagin).
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159 ccb 1.188 * cBUCCANEER: statistical model building, optimised for experimental
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160 ccb 1.180 phasing. (Kevin Cowtan)
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161 ccb 1.188 * CRUNCH2: direct mothod experimental phasing as part of CRANK (Jan
162 Abrahams)
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163 nds65 1.183 * CTRUNCATE: New program for Intensity to Structure Factor conversion and
164 checking data quality (Norman Stein).
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165 pjx 1.191 * DBCCP4I: new database server for CCP4i, which includes a graphical
166 viewer for CCP4i projects plus other tools. (Wanjuan Yang & Peter Briggs)
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167 ccb 1.200.2.3 * IMOSFLM: imported imosflm 1.0.0
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168 rmk65 1.181 * MrBUMP: Automated molecular replacement, search model retrieval and
169 search model preparation for molecular replacement.
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170 pjx 1.151 * MTZ2CIF: new program for generating mmCIF reflection files suitable
171 for deposition, intended to replace OUTPUT CIF option of MTZ2VARIOUS.
172 See program documentation for more information. (Peter Briggs)
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173 ccb 1.200.2.3 * PARROT: automatic density modification and phase improvement (Kevin Cowtan)
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174 ccb 1.180 * PISA: the standalone version of the Protein Interfaces, Surfaces and
175 Assemblies server. (Eugene Krissinel) -- optional
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176 nds65 1.200.2.5 * POINTLESS: Laue and Patterson group determination, v1.2.23. (Phil Evans)
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177 gwin 1.200 -- optional
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178 rmk65 1.181 * R500: new program for correcting REMARK 500 lines in PDB files.
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179 nds65 1.183 * RAPPER: conformer modelling through sampling residue rotameric states.
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180 ccb 1.180 (Nicholas Furnham, Paul de Bakker, Mark DePristo, Reshma Shetty,
181 Swanand Gore and Tom Blundell) -- optional
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182 ccb 1.188 * cSEQUINS: Statistical protein chain tracing (Kevin Cowtan)
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183 pjx 1.163 * SEQWT: new utility to estimate protein molecular weight from the
184 sequence. (Eleanor Dodson)
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185 pjx 1.159 * SYMCONV: new utility program for interrogating the CCP4 symmetry
186 libraries. (Peter Briggs)
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187 rmk65 1.181 * XIA2: Automated data reduction system designed to work from raw
188 diffraction data and a little metadata, and produce usefully reduced
189 data in a form suitable for immediately starting phasing and structure
190 solution.
|
191 pjx 1.148
192 * Graphical User Interface:
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193 ccb 1.192 * Version 2.0
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194 pjx 1.167 * Modules can now include "subfolders" of tasks to help with grouping
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195 pjx 1.168 related tasks together within a module. These can also be included in
196 task packages that are exported - however developers should note that
197 packages created with subfolders are NOT backwardly compatible with
198 older versions of CCP4i.
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199 pjx 1.165 * A right-mouse click on the job list presents a "context menu" offering
200 job manipulation options for the current selection (for example,
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201 pjx 1.166 rerun or delete jobs). Double-clicking with the left-mouse on a
202 specific job automatically tries to "rerun" that job.
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203 pjx 1.175 * Options for customising the colours of jobs displayed in the job list
204 can be accessed via the "System Administration" and the context menu
205 described above.
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206 pjx 1.166 * Viewing files from job in some cases (e.g. Refmac5) now also provides
207 options (when possible) to launch "plugin" applications (e.g. Coot,
208 CCP4mg) preloaded with the appropriate data.
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209 pjx 1.160 * New option to re-import tasks that have already been installed in a
210 previous version of CCP4 (e.g. Arp/Warp): accessed via the
211 "Install/Uninstall Tasks" interface in the "System Administration"
212 menu. (Note that this function requires the user to have permissions
213 to write files to the CCP4i area.)
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214 pjx 1.161 * ccp4ish can be run with a "-import_packages <old_ccp4>" option, which
215 attempts to automatically copy any tasks previously installed in the
216 CCP4 installation in <old_ccp4>, and add them to the current CCP4i
217 installation.
|
218 pjx 1.153 * Disabled ("greyed out") tasks can be enabled by setting the appropriate
219 option in the "Configure Interface" window
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220 pjx 1.172 * MOSFLM-in-batch: now recognises keywords SYNCHROTRON POLARISATION,
221 DISPERSION and DIVERGENCE (used for data collected at a synchrotron)
222 and POSTREFinement keywords WIDTH, MOSADD and MOSSMOOTH.
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223 ccb 1.200.2.3 * PARROT: new interface for the PARROT program.
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224 pjx 1.154 * PISA webservice: the EBI Protein Interfaces Surfaces and Assemblies
225 webservice can be launched from the "Structure Analysis" and "Program
226 List" modules
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227 nds65 1.183 * POINTLESS: new interface to the POINTLESS program (NB this supersedes
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228 pjx 1.179 the prerelease interfaces: "Determine Laue Group", "Test Alternative
229 Indexing" and "Check Centre of Symmetry" - these interfaces can still
230 be accessed e.g. for reviewing old jobs, but are now deprecated).
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231 pjx 1.152 * "SFs for Deposition" task (mtz2cif) now uses MTZ2CIF program rather
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232 pjx 1.166 than MTZ2VARIOUS.
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233 pjx 1.157 * GetMtzColumnResolution: new command that fetches the maximum and
234 minimum resolution limits for a specific column in an MTZ file.
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235 pjx 1.169 * CURRENT_PROJECT and MG_CURRENT_PROJECT parameters are now stored in
236 status.def (previously in directories.def).
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237 pjx 1.177 * XIA2: new interface to the XIA2 automated data processing package.
238 * Annotated HTML logfiles are generated after each program run using
239 the "baubles" program.
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240 nds65 1.183 * Made a new task for job colourisation so it is more visible outside
241 the big configure task.
242 * Added Dyndom and Chooch interfaces files and added the tasks into
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243 fr45 1.178 Program list.
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244 rmk65 1.181 * Added the MrBUMP (automated molecular replacement) interface.
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245 nds65 1.183 * Added new Map & Mask Utilities task to calculate an omit map using
246 Sfcheck.
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247 pjx 1.186 * Clipper Utilities: this module has been removed and the Clipper-based
248 tasks have been moved to other modules, mainly "Reflection Data
249 Utilities" and "Map & Mask Utilities".
|
250 fr45 1.190 * Added new interface for the existing getax program.
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251 pjx 1.196 * New task interfaces added to "Data Reduction" module ("Check Data
252 Quality" folder): "Analysis with ctruncate" and "Analysis with sfcheck"
253 allow experimental data to be characterised more easily.
254 * New task interface added to "Molecular Replacement" module ("Analysis"
255 folder): "Self RF with molrep" provides interface to the self-rotation
256 function calculation of Molrep.
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257 pjx 1.197 * autoSHARP: new interface to SHARP/autoSHARP. Needs a separate install
258 of SHARP/autoSHARP. (Clemens Vonrhein)
|
259 pjx 1.148
260 * Documentation:
|
261 pjx 1.149 * AREAIMOL: added figures to clarify the definitions of the different
262 surface types.
|
263 nds65 1.183 * MrBUMP: documentation for MrBUMP, automated molecular replacement
|
264 rmk65 1.181 program.
|
265 pjx 1.148
266 * Withdrawal:
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267 mdw 1.174 * The following programs have been placed in deprecated/src for future
268 removal: BEAST (replaced by Phaser), ROTAPREP (replaced by Combat),
269 ARP_WATERS (use latest ARP/wARP), BPLOT, POLYPOSE, RSEARCH,
270 RESTRAIN.
271 * The following X-windows programs have been taken out of the build
272 procedure, prior to future removal: XLOGGRAPH (replaced by loggraph),
273 XDLMAPMAN, XDLDATAMAN, IPDISP (replaced by idiffdisp)
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274 pjx 1.148
275 * Examples:
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276 ccb 1.200.2.2 * phaser_EP.exam: new example for Phaser 2.1.4, using a sulfur-SAD
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277 mdw 1.174 dataset for bovine cubic insulin.
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278 ccb 1.180 * pointless.exam: new examples for pointless
279 * rampage.exam: new example for rampage mode of rapper
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280 ccb 1.192 * refmac_sad: new example for refmac SAD target function
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281 gwin 1.200.2.4 * acorn: new example running from 1 Zn atom (Deuterolysin)
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282 pjx 1.148
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283 mdw 1.132 Summary of significant changes to CCP4 at version 6.0
|
284 mdw 1.92 -----------------------------------------------------------
285
286 * Building etc.:
|
287 ccb 1.97 * Clipper/fftw built by default
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288 mdw 1.101 * cctbx/phaser are included as separate packages. The main
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289 pjx 1.121 CCP4 build will build them if these packages are included.
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290 mdw 1.101 * There are a number of fixes for the AIX build.
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291 pjx 1.103 * to_small_refmac.csh/to_big_refmac.csh: shell scripts to
292 reduce and restore the array sizes for Refmac5 prior to
293 compilation (in $CPROG/refmac5_/)
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294 mdw 1.105 * A new ccp4.setup-zsh for ZSH users (Bill Scott)
|
295 mdw 1.142 * --with-x is now the default; use --disable-x if you have
296 problems with the X-windows build
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297 pjx 1.145 * The script "patch_ccp4.sh" in $CETC can be used to
298 automatically download and apply available source code fixes
299 to the suite for UNIX-based systems. Note that any
300 recompilation must still be performed manually afterwards -
301 see Appendix M of the CCP4 installation instructions.
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302 mdw 1.92
303 * Program changes:
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304 mdw 1.141 * ANISOANL: now checks for non-positive-definite Us in XYZIN
305 and lists to log file (all options)
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306 pjx 1.129 * AREAIMOL: new REPORT keyword allows control of output for
307 contact areas and reporting of area by residue
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308 mdw 1.144 * CIF2MTZ: several new column labels added, including anomalous
|
309 mdw 1.101 * COORD_FORMAT: new keyword FIXBLANK
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310 mdw 1.92 * DM: program now produces a data harvesting file
|
311 pjx 1.129 * MapSlicer: supports reading and display of mask files (new
312 "mask" mode); displays "greyscale" view superimposed on
313 contours; saves user preferences for contour levels and other
314 settings between sessions.
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315 pjx 1.98 * MTZ2VARIOUS: if F(+) and F(-) are input for SHELX output then
316 rescaling is done within the program to produce
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317 pjx 1.135 pseudo-intensities; OUTPUT CIF option updated to use tokens
318 from the PDB exchange dictionary for anomalous data and HL
319 coefficients.
|
320 mdw 1.101 * PDBCUR: new keywords SUMMARISE, DELHYDROGEN, MOSTPROB, CUTOCC,
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321 pjx 1.121 and TRANSLATE (MDW)
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322 pjx 1.171 * PDB_EXTRACT: new version 2.0
|
323 pjx 1.93 * PDBSET: new function ATRENUMBER (renumber atoms sequentially
324 without gaps in output file)
|
325 pjx 1.123 * PEAKMAX: new keyword EXCLUDE (turns suppression of peaks at the
326 edge of the map on or off)
|
327 mdw 1.142 * REFMAC: new version 5.2.0019
328 * MOLREP: new version 9.0.09
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329 mdw 1.132 * MOSFLM: new version 6.2.5
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330 mdw 1.142 * SFCHECK: new version 7.0.18
|
331 mdw 1.101 * SFTOOLS: new options LIST/SET DCELL/DWAVE for dataset information
|
332 ccb 1.126 * Matthews_coeff: outputs the Kantardjieff and Rupp resolution based
333 probabilities
|
334 fr45 1.112 * FFTBIG replaces FFT
335 * SCALEPACK2MTZ SYMM keyword not compulsory anymore, will try to pick up
336 spacegroup in the input file.
|
337 mdw 1.132 * TLSANL: ANISOU line in XYZOUT is now adjusted according to ISOOUT
338 keyword. Summary tags used to highlight important quantities.
|
339 mdw 1.92
340 * Library changes:
|
341 pjx 1.93 * CCPERR/ccperror: each time ccperror is called it invokes a
342 user-defined callback function which has previously been set
343 using new C library function "ccp4SetCallback".
|
344 mdw 1.101 * CCTBX library included as a separate package (Paul Adams,
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345 pjx 1.121 Ralf Grosse-Kunstleve et al)
|
346 mdw 1.92
347 * New programs:
|
348 mdw 1.127 * BP3: multivariate likelihood substructure refinement and phasing
349 of S/MIR(AS) and/or S/MAD (Raj Pannu)
|
350 pjx 1.140 * CHAINSAW: new molecular replacement utility that mutates a pdb
351 file to poly-serine using a sequence alignment (Norman Stein)
352 * PDB_MERGE: jiffy to merge two PDB files (Martyn Winn)
353 * PHASER 1.3: molecular replacement (Randy Read et al)
|
354 mdw 1.143 * PIRATE (cpirate): statistical phase improvement (Kevin Cowtan)
|
355 pjx 1.140 * SUPERPOSE: secondary structure alignment (Eugene Krissinel)
|
356 mdw 1.92
357 * Graphical User Interface:
|
358 pjx 1.171 * Version 1.4.4.1
|
359 pjx 1.138 * AREAIMOL: new option to generate pairwise area differences for
360 "molecules" (defined as arbitrary groups of chains) in a PDB file.
|
361 mdw 1.101 * CRANK: interface to automated structure solution via experimental
|
362 pjx 1.104 phasing (currently SAD, SIR and SIRAS data)
|
363 pjx 1.108 * SHELX C/D/E: interface to running the SHELX C, D and E programs
364 standalone or as a pipeline in order to perform heavy atom
365 search and phasing
|
366 pjx 1.136 * CHAINSAW: interface to new program of the same name; mutates a pdb
367 file to poly-serine using a sequence alignment for molecular
368 replacement
|
369 pjx 1.171 * PISA webservice: the EBI Protein Interfaces Surfaces and Assemblies
370 webservice can be launched from the "Structure Analysis" and "Program
371 List" modules (added in 6.0.2)
|
372 pjx 1.120 * Scale and Merge Intensities (SCALA): option to output Scalepack
373 formatted reflection files suitable for input into SHELX or SOLVE
374 (corresponds to OUTPUT POLISH UNMERGED option of SCALA)
|
375 pjx 1.121 * Run Remote Jobs: option to use either rsh or ssh to run jobs on
376 remote machines.
|
377 pjx 1.124 * Output in different map formats: the interface should now only
378 offer output in the formats (O, QUANTA) that can actually be
379 created with the user's setup
|
380 pjx 1.116 * CreateLabinLine4: extended version of CreateLabinLine that allows
381 groups of up to four related labels to be specified, for example
|
382 pjx 1.146 H-L coefficients or F(+)/sigF(+) and F(-)/sigF(-) groups. This
383 command also supports a -command option similar to other
384 CreateLine-type commands. See the documentation for details.
|
385 pjx 1.96 * FindExecutable: new command, return full path of a program
386 executable
|
387 pjx 1.93 * Install Task: export task now allows save/restore of parameters;
|
388 pjx 1.121 tasks can be defined as basename/directory pairs; version number
389 included in archive filename.
|
390 pjx 1.93 * Logfile viewer: when viewing a long file, there is now the
391 option to look at the previous frame as well as the next one.
|
392 pjx 1.116 * MTZ handling: new commands GroupMtzCols, MtzColSameDataset,
393 GetMtzColType, GetMtzGroupByType.
|
394 pjx 1.93 * WarningMessage: has new options -image, -font and -color
395 * Superpose: when fitting atoms from one PDB file to another, atom
396 numbers given by the user now refer to those specified in the file
397 (rather than to the positions in the file)
|
398 pjx 1.104 * types.def: added new types "_res_file" (ShelxD result file) and
399 "_phs_file" (XtalView phases file)
|
400 pjx 1.121 * File Selection for Windows: drive can also be chosen from the file
401 browser.
|
402 pjx 1.107 * Disabled tasks: some task interfaces will be unavailable to users
403 if "prerequisites" (as defined in the taskname_prereq procedure in the
404 task interface file) are not found on the user's system.
405 "Disabled" means that the task button will be non-functional and the
|
406 pjx 1.113 text will be greyed-out.
407 Check the documentation $CCP4I_HELP/general/additional.html for
408 information on how to enable these tasks.
|
409 fr45 1.109 * Project Switching: Having a small menu button enabling to instantly
410 switch between projects without passing through "directories" interface
|
411 pjx 1.116 * Database search/sort: Having a new Button search/sort popping up a window
412 enabling users to do various kinds of simple/advanced search and/or sorting
413 also be able to refine sorts or searches.
|
414 pjx 1.137 * CreateToggleFrame: new option -justify allows programmer to specify the
415 positioning of the subframes (left, right or center).
|
416 mdw 1.92
417 * Documentation:
|
418 pjx 1.95 * Added documentation on adding doc comments for CCP4i core commands
419 ($CCP4I_HELP/progdocs/documenting.html)
|
420 pjx 1.117 * alternate_origins.html: updated with spacegroup numbers, information
421 about alternative settings and Hermann-Mauguin symbols
|
422 pjx 1.128 * Loggraphs: documentation for TABLE, GRAPHS, SCATTER etc now in
423 loggraphformat.html (see "File Formats" section)
|
424 mdw 1.92
425 * Withdrawal:
|
426 ccb 1.122 * fft (replaced by fftbig )
|
427 mdw 1.92
428 * Examples:
|
429 mdw 1.142 * abs, bp3, chainsaw, pdb_merge, phaser, pirate, superpose examples added
430 * New examples for using python interface to cctbx and phaser
431 (cctbx_py_test.exam and phaser_py_test.exam)
|
432 mdw 1.92
|
433 mdw 1.61 Summary of significant changes to CCP4 at version 5.0
434 -----------------------------------------------------
435
436 * Building etc.:
437 * configure: convex, stardent, titan, concentrix, ultrix and esv systems
438 all removed.
|
439 pjx 1.65 * Intel compilers: support for Intel compilers under Linux has been
440 implemented; use "configure linux_intel_compilers [options]"
|
441 ccb 1.72 * Intel compilers: support for Intel compilers under Linux on IA64
442 machines has been implemented (by SGI Japan); use "configure
|
443 ccb 1.82 ia64_linux_intel [options]"
|
444 ccb 1.72 * gnu compilers: IA64 support implemented; use "configure linux [options]"
|
445 pjx 1.75 (warning 3.0 broken)
|
446 ccb 1.83 * FreeBSD build: now can use g77 (thanks to Tim Gruene)
|
447 pjx 1.75 * LAPACK/BLAS: CCP4 configuration for NetLib BLAS and LAPACK now includes
448 all available functions (single, double, complex and double complex)
|
449 mdw 1.61
450 * Program changes:
|
451 pjx 1.63 * ACORN: updated version: 1) faster translation function using FFT (TRAN).
452 2) Phase errors can be calculated if true phases are input (LABIN).
|
453 mdw 1.61 * AMORE: substantially updated version: 1) Now estimates memory allocation
454 automatically (manual assignment is still available). 2) TABFUN: new
455 keyword BTARGET to adjust model B factors; NORMALISE keyword to generate
456 normalised model sf's. 3) CLMN: extended number of Bessel functions used
457 to generate spherical harmonics. 4) Fixes to Locked Rotation Function.
458 5) TRAFUN: can work with non-crystallographic translation.
|
459 pjx 1.63 * ASTEXVIEWER: please note updated conditions of use (see AstexViewer
460 documentation).
|
461 mdw 1.74 * BEAST: an MPI version has been added, see $CPROG/beast_/beast_MPI
|
462 pjx 1.77 * CAD: new keywords DRENAME, XNAME and DPNAME. SCALE keyword updated
463 to accept anisotropic B values.
|
464 mdw 1.70 * CIF2MTZ: new keyword NAME
|
465 mdw 1.88 * COMBAT: 1) new keyword NAME, 2) new option INPUT XDSASCII for reading
466 file XDS_ASCII.HKL from CORRECT stage of XDS
|
467 mdw 1.61 * COORDCONV: new option INPUT SNB reads SnB peaks files.
468 * DISTANG: changed format of symmetry/translational operators in logfile.
469 Note that the OUTPUT DISTOUT option must now be used to generate
470 output appropriate for input to WATERTIDY.
|
471 mdw 1.70 * DTREK2MTZ: new keywords NAME, WAVE (specifies wavelength of dataset).
472 * DTREK2SCALA: new keyword NAME
473 * F2MTZ: new keyword NAME
|
474 mdw 1.74 * FSEARCH: an MPI version has been added, see $CPROG/fsearch_mpi.f
|
475 mdw 1.61 * LSQKAB: increased array sizes (NATOM to 40000, NRS to 13999).
476 * MLPHARE: significant changes including:
477 1. ISOE/ANOE now taken (correctly) from last REFINEMENT cycle
478 2. Checks if two input sites are too close (prevents failures after
479 RANTAN/SHELX/ACORN if peak search puts a site close to its symmtery
480 related neighbour)
481 3. Checks if anom refinement is requested but all AOCC are zero; if
482 OCC is non-zero when only anomalous diffs are used.
|
483 pjx 1.71 * MAPSLICER/CCP4MAPWISH: 1) Default view changed to be "right-handed",
484 with option to chnage to "left-handed" view; 2) In "Harker" mode
485 axes are labelled "UVW" rather than "XYZ"; 3) new option to generate
486 contours starting from mean density in the map.
|
487 awa 1.73 * MOLREP: new version 7.5.01.
|
488 ccb 1.131 * MOSFLM: new version 6.2.5
|
489 pjx 1.62 * OASIS: new version 1.2.2.
|
490 pjx 1.66 * POLARRFN: new version extended to order 100 in sph. harm. expansion (from
491 Ian Tickle). This allows larger integration radius without loss of
492 resolution.
|
493 mdw 1.61 * PROFESSS: updated version outputs PDB file with the final atoms
|
494 pjx 1.68 * RASMOL: version 2.7.2.1.
|
495 mdw 1.70 * REBATCH: new BATCH XNAME keyword
496 * REFMAC: version 5.2.
|
497 pjx 1.62 * ROTAMER: updated version has for each Phe and Tyr rotamer Chi(1),Chi(2)
498 a symmetric one Chi(1),-Chi(2).
|
499 mdw 1.70 * RWCONTENTS: now uses residues from the monomer library: note that numbers
500 of hydrogens associated with CYS is now 4 (was 5), with HEM is 30 (was
501 17). Also, calculates I000 (square of atomic formfactors) from input
|
502 pjx 1.62 coordinates.
|
503 ccb 1.125 * SCALA: version 3.2.14
|
504 mdw 1.70 * SCALEPACK2MTZ: new keyword NAME
|
505 pjx 1.62 * SFALL: new keyword NAME
|
506 pjx 1.67 * SFCHECK: version 6.0.4
|
507 pjx 1.90 * SORTMTZ: new keyword VRSET.
|
508 mdw 1.61 * TRUNCATE: minor change to labels on cumulative intensity distribution
509 graph.
510 * WATERTIDY: no longer accepts the logfile output from DISTANG as input,
511 due to changes in DISTANG. Use the OUTPUT DISTOUT option of DISTANG
512 to prepare appropriate input for WATERTIDY.
513
514 * Library changes:
|
515 pjx 1.65 * New Core Libraries: new underlying C language libraries have been
516 introduced:
517 * CMTZLIB: MTZ file I/O and reflection data handling
518 * CMAPLIB: CCP4 mapfile I/O
519 * MMDB: Coordinate data handling (C++)
520 * CCP4_PARSER: CCP4 keyword parser
521 * CSYMLIB: CCP4 symmtery handling functions
522 * CCP4_GENERAL, CCP4_PROGRAM: utilities for providing CCP4 program
523 environment
524 * CCP4_ARRAY: resizeable array implementation
525 * CCP4_UNITCELL: utilities for manipulations based on cell parameters
526 * CVECMAT: vector and matrix manipulations
527 * LIBRARY_UTILS: general platform-independent utilies (date, filename
528 manipulations, etc)
529 * LIBRARY_FILE: general file I/O
530 * LIBRARY_ERR: functions for library error handling
531 These functions can be invoked from C/C++ applications (see e.g. NCONT,
532 PDBCUR, MTZDIFF). There are also a number of new C language libraries
533 providing Fortran interfaces:
534 * CCP4_DISKIO_F: Fortran API for file i/o
535 * CCP4_GENERAL_F: Fortran API to utilities providing CCP4 program
536 pjx 1.65 environment
537 * CCP4_UNITCELL_F: Fortran API to utilities for manipulations based
538 on cell parameters
539 * CCP4_PARSER_F: Fortran API for CCP4 keyword parser
540 * CMTZLIB_F: replicates old mtzlib.f
541 * CMAPLIB_F: replicates old maplib.f
542 * CSYMLIB_F: replicates old symlib.f
543 A number of old library files have been altered:
544 * ccplib.f: many functions replaced by CCP4_GENERAL_F
545 * library.c: withdrawn
546 * parser.f: many functions replaced by CCP4_PARSER_F
547 * rwbrook.f: withdrawn; replaced by Fortran API in MMDB
548 The Fortran APIs provided by the new libraries should match that from
549 the old (pre-5.0) libraries, and existing Fortran applications should be
550 unaffected by these changes.
551 The libraries build into three files: libccp4c (containing the core C
552 libraries in the first section above, except MMDB), libmmdb (containing
553 the MMDB libraries only), libccp4f (containing the Fortran and Fortran
554 API functions).
|
555 mdw 1.85 * Clipper: new C++ library for reflection and map handling (Kevin Cowtan)
|
556 pjx 1.87 * DNA_OUTPUT: library routines to support the DNA Project (see
557 http://www.dna.ac.uk/)
|
558 mdw 1.85 * FFTW: Fastest Fourier Transform in the West. Currently only used by
559 Clipper library.
|
560 mdw 1.70 * Monomer library: updated for REFMAC 5.2.
|
561 mdw 1.61
562 * New programs:
|
563 pjx 1.75 * BULK: bulk solvent correction for translation search and rigid body refinement
564 steps of AMoRe (A. Fokine, A. Urzhumtsev, G. Capitani, M.G. Grutter)
|
565 pjx 1.64 * DTREK2SCALA: convert integrated intensity and header files from D*TREK
566 into a multi-record mtz file (Gwyndaf Evans)
|
567 pjx 1.76 * EXTENDS: extend Fourier maps and compute standard uncertainty of electron
568 density (Phil Evans, Ian Tickle).
|
569 pjx 1.62 * MTZDIFF,MAPDIFF,PDBDIFF: utilities to examine differences between
570 pairs of MTZ, map and PDB files respectively (Peter Briggs)
|
571 mdw 1.80 * NCONT, PDBCUR and COORD_FORMAT: new coordinate utility programs based on the
|
572 pjx 1.62 MMDB library (Eugene Krissinel)
|
573 pjx 1.90 * PDB_EXTRACT 1.5: programs for extracting deposition data from logfiles
|
574 pjx 1.77 (RCSB)
|
575 mdw 1.78 * pdb-mode.el: major mode for editing Protein Data Bank files in
576 Emacs (Charlie Bond). There is also a simpler version pdb.el which
577 is mainly for highlighting (Martyn Winn). See also cif.el (Martyn Winn).
|
578 mdw 1.81 * TLSEXTRACT: a jiffy for extracting TLS parameters from the REMARK 3 records
579 of a PDB file (Jay Painter). Interfaced in Edit/Create TLS File.
|
580 pjx 1.66 * TOPDRAW: sketchpad for drawing topology cartoons of proteins
581 (Charlie Bond)
|
582 mdw 1.61
583 * Graphical User Interface:
|
584 pjx 1.89 * CCP4i version 1.3.18
|
585 pjx 1.62 * types.def: new widget types "varbutton", "postmenu", "selmenu",
586 "exframe_rb";
587 new file types "_MGPY_file" (molecular graphics script),
|
588 mdw 1.70 "_pickle_file" (MG save status), "_pic_file" (screen snapshot),
589 "_rlist_file" and "_sol_file" (Phaser solution files);
|
590 pjx 1.62 new MTZ label type "_mtz_label_e" (normalised structure factor).
|
591 pjx 1.75 * Help facilities: message line help is now also displayed as
592 "bubble help". Turn this feature off in "Configure Interface".
|
593 pjx 1.63 * Command templates (com files) can use ampersand ("&") as a
594 continuation character for both standard template lines and
595 LABELLINE commands.
|
596 pjx 1.62 * View Files from Job: when additional log and loggraph files are
597 output from a job, these are now grouped under submenus called
598 "Additional log files" and "Additional log graphs" (instead of
599 being in the main list of output files).
|
600 pjx 1.63 * Log file viewers: added option to use text browser to display
|
601 pjx 1.62 logfiles.
|
602 pjx 1.77 Up and down arrow keys enable single-line scrolling (Steven Ness).
|
603 mdw 1.61 * DbLockFilePid: returns pid which "owns" current database lock.
|
604 pjx 1.62 * CentreWindow: centres a window over a parent, or screen centre.
605 * MakeLock/LockStatus/DeleteLock/CreateLock: new procedures for
606 dealing with file locks.
|
607 pjx 1.86 * WriteImage: new command. Allows an image (any type supported by the
608 Tcl "image" command) to be displayed in a task interface.
|
609 pjx 1.66 * New module: "Graphics and Viewing Utilities" contains AstexViewer,
610 Loggraph, MapSlicer, RasMol (Unix only) and TopDraw.
|
611 pjx 1.62 * Amore: low resolution cutoff defaults to 15.0A, and is no longer
|
612 pjx 1.66 read from the input MTZ file. Solution files (.mr) include
613 SYMMETRY, CELL and RESOLUTION information in the header -
614 SYMMETRY from .mr file will be checked against that used for
615 Amore runs.
616 * Areaimol interface: new interface to calculate protein accessible
617 surface areas and area differences.
|
618 pjx 1.67 * ClustalW interface: new interface (nb the ClustalW program is not
619 distributed with CCP4).
620 * Data Harvesting Management Tool: new interface to review and
621 manage harvesting files produced from harvesting programs.
|
622 pjx 1.63 * Distang: removed from Program List, there is no dedicated Distang
623 task.
|
624 mdw 1.61 * Import Unscaled Data (combat): added option to enter wavelength.
625 * PrepHaData: SHELX options expanded to prepare data for either
626 SHELXS or SHELXD.
|
627 pjx 1.62 * Mlphare: output Hendrickson-Lattmann coefficients by default.
|
628 pjx 1.75 * Modeller: interface updated to work with either Modeller 6 (default)
629 or Modeller 4.
|
630 pjx 1.62 * MOSFLM interface: new interface to run MOSFLM in batch mode.
|
631 pjx 1.75 * Merge Monomer Libraries: a simpler interface has been implemented to
632 replace the old "AddDict" interface for merging monomer files.
633 "AddDict" can still be accessed via the Monomer Library Sketcher.
634 * Refmac5: substantial update to the Refmac interface.
|
635 pjx 1.63 * 'Old' Refmac/Protin: interfaces are retained to allow users to
636 review parameters from old jobs, but the tasks cannot be run as
637 the programs have been withdrawn.
|
638 pjx 1.62 * Scala: new option to accept observations previously flagged as
639 rejected by MOSFLM (ACCEPT keyword in SCALA program).
|
640 pjx 1.71 * Sketcher: 1) Report name of monomer and source file in sketcher
641 window; 2) Run imported CIF file through Libcheck automatically
|
642 pjx 1.75 * Edit/Create TLS File: now has "Reset" button to clear previously set
|
643 mdw 1.81 parameters. It can also extract TLS groups from the REMARK 3 records
644 of PDB format file. It will optionally handle TLS parameters.
|
645 mdw 1.61
646 * Documentation:
|
647 mdw 1.85 * symmetry.html, cheshirecell.html: new documents
|
648 pjx 1.62 * Sketcher: added to index of programs.
|
649 mdw 1.61
650 * Withdrawal:
651 * ABSURD, UNDUPL, MADLAT: programs for MADNES
652 * EXTEND: use MAPMASK
|
653 pjx 1.77 * REFORM: obsolete
|
654 mdw 1.61 * RWDICT: use MAKEDICT
655 * MSTAMP: obsolete
|
656 pjx 1.62 * PROTIN/REFMAC: use refmac5
|
657 mdw 1.61
658 * Examples:
|
659 mdw 1.70 * RNASE.PDB: naming of waters ("HOH") updated to be consistent with new
660 monomer dictionary, and with convention used in toxd.pdb: OW* changed
661 to O1, with one oxygen per "residue".
|
662 mdw 1.61
|
663 pjx 1.58 Summary of significant changes to CCP4 at version 4.2.1
664 -------------------------------------------------------
665
666 * Building etc.:
|
667 pjx 1.60 * General: running "make install" failed if executed immediately after
668 the configure step; now fixed.
|
669 pjx 1.58 * IRIX: fixed building of shared library by default on IRIX 6.5.
670 * OSF1: 1) new configure option --non_shared prevents linking executables
671 against shared libraries (including system libraries);
672 2) "-D__V40_OBJ_COMPAT -nointrinsics -D" compiler flags removed for
673 Tru64 V5.0.
674 * Mapslicer configuration: fixed problem with configure looking for Tk
675 library with the wrong file extension.
676
677 * Program changes:
678 * ASTEXVIEWER: .jar file updated to allow the viewer to run as
679 standalone.
680 * MOSFLM: version 6.2.2
|
681 pjx 1.59 contains fix for R/H3x problems.
|
682 pjx 1.58 * REFMAC5: version 5.1.24
683 * SCALA: version 3.1.9
684
685 * Library changes:
686 * CCIFLIB: fixed bug with passing fixed length for Fortran strings in
687 s/r ccp4ccif_setup_context.
688 * MAPLIB: five of the ENTRYs have been renames as they exceed 31
689 characters in length.
690 * PARSER: number of characters increased to prevent filename truncation
691 when filenames are read from the keyworded input.
692 * RWBROOK: fixed problem when spacegroup name is longer than space
693 permitted in PDB file.
694 * SYMLIB: increased the hashing parameter KPRI in CCP4_HASH_... routines
695 to 5003, to cope with maximum number of batches in SCALA (5000).
696
697 * Graphical User Interface:
698 * Version 1.3.8.
699 * General: Kill Job function updated to work under Mac-OSX and SunOS
700 * General: fixed problems starting help pages from KDE on Linux
701 * General: fixed problem with restarting task interfaces after being
702 closed using the Window Manager rather than the CCP4i "Close" button
703 pjx 1.58 * Refmac5: fixed problem with interface requesting harvesting information
704 in Review mode.
705 * Scala: new option to automatically combine all input datasets into
706 a single output dataset.
707 * Monomer Library Sketcher: 1) fixed problem with "unknown option -dash"
708 for Tk versions earlier than 8.3; 2) fixed problem with delocalised
709 and aromatic bond types not being written to bondlist.cif.
|
710 pjx 1.48
|
711 pjx 1.53 Summary of significant changes to CCP4 at version 4.2
712 ------------------------------------------------------
713
714 * Building etc.:
|
715 pjx 1.56 * IRIX 6.5: changed to n32 compilation.
|
716 pjx 1.53 * LAPACK: the BLAS and LAPACK libraries are now included in the CCP4
717 installation by default. If a suitable system-specific LAPACK library
718 is not found at configuration time then the version from Netlib will
719 be built. Use the --disable-lapack configure flag to suppress inclusion
720 of the LAPACK library, or the --with-netlib-lapack flag to force
721 building of the Netlib versions.
722 * configure: Have added an extra keyword --with-warnings. If this is not specified
|
723 ccb 1.54 some systems will be compiled with a -w which will suppress compiler warnings
|
724 pjx 1.53 for the main suite.
|
725 ccb 1.54 * xdlmapman: now builds using a m4 preprocessor stage to allow system
726 dependent FORTRAN file record sizes.
|
727 pjx 1.53
728 * Program changes:
729 * ALMN: automatically checks that input files have consistent indexing,
730 and suggests reindexing operation if they do not.
731 * AREAIMOL: calculates contact areas as well as ASA; allows large probe
732 sizes (up to 25A radius); new MATCHUP option for use with DIFFMODE
733 COMPARE e.g. for different confirmations; ignores hydrogens in input
734 files; improved handling of unknown atom types.
735 * ARP_WATERS: The CCP4-distributed version of arp_warp (v5.0) has been
736 renamed to "arp_waters". Example scripts, documentation etc has also
737 been renamed accordingly.
738 * BAVERAGE : htmlized the output.
739 * COMBAT: the MTZF option now accepts F(+) and F(-) as an alternative
740 to mean F. MISBATCH option removed: now only outputs batches which
741 are present in the input file. INPUT USER option fixed (was broken).
742 "I" decsriptors in FORMAT statements are automatically converted to
743 the appropriate "F" format. Fixed incorrect lattice type setting for
744 centred spacegroups in MTZ files.
745 * DTREK2MTZ: previously, handled files incorrectly if there was no
746 anomalous data - this feature now fixed.
747 * DYNDOM: New version 1.2
|
748 pjx 1.55 * ECALC: LABIN will now take DPH/SIGDPH, new MODD keyword.
|
749 pjx 1.53 * F2MTZ: for USER defined input, "I"'s in the Fortran FORMAT
750 statement are now automatically changed to the appropriate "F"
751 descriptors.
|
752 pjx 1.56 * FFFEAR: Upgrade to version 1.9
|
753 pjx 1.53 * FFT/FFTBIG: the default axis ordering is Z,X,Y for P1, monoclinic
754 space groups, and space groups 16, 17 and 18, and Y,X,Z for all
755 higher symmetry space groups. Default map volume in FFTBIG is now
756 always the whole unit cell.
757 * GENSYM: fix to SPHER ORTHOGONAL option.
758 * MATTHEWS_COEF: Added keyword AUTO that will produce a table
759 of the possible number of molecules in the Asym unit.
760 ** MOLREP: Molrep now uses keywords and command line options.
|
761 pjx 1.91 Also updated to verion 8.2.01.
|
762 mdw 1.57 * MOSFLM: version 6.2.1
|
763 pjx 1.53 * MTZ2VARIOUS: Added OUTPUT MAIN option.
764 * OASIS: new keywords RES and SIG, increased limit on number of
765 reflections, plus a number of bug fixes.
|
766 mdw 1.57 * REFMAC: version 5.1.19
|
767 pjx 1.53 * REVISE: Now produces graphs of the correlations between anomalous
768 differences for different wave lengths and the rms Dano; the
769 tables of ratioes of data sets split the data into 15 bins (was 10).
|
770 pjx 1.56 * SCALA: new version 3.1.4.
|
771 pjx 1.53
772 * Library:
773 * MAPLIB: Reinitialise mean and RMS density when creating multiple
774 maps in a single program run.
775 * PXXML: new subroutine library for writing XML.
776 * RWBROOK: s/r PDBREAD gives tries to identify ambigious atom names
777 like AC5* and NO4* when no element name is supplied.
778 * SYMOP: Hexagonal spacegroups 146, 148, 155, 160, 161, 166 and 167
779 are now refered to by the symbols H.
780 * unix.m4, vms.for, w32mvs.f: CCPOPN won't print error message for
781 file opening error if called with IFAIL=2.
|
782 ccb 1.54 * xdl_view: new version 4.5
|
783 pjx 1.53
784 * New programs:
|
785 ccb 1.54 * ABS: program to determine the hand of the heavy atom substructure
786 (Q.Hao)
|
787 pjx 1.53 * ACORN: ab initio procedure for the determination of protein structure
788 at atomic resolution (Yao Jia-Xing)
|
789 pjx 1.55 * ASTEXVIEWER: Java application for viewing proteins, ligands and electron
790 density maps (Mike Hartshorn)
|
791 pjx 1.53 * BEAST: Brute-force molecular replacement with Ensemble Average Statistics,
792 Maximum likelihood-based molecular repaclement (Randy Read)
793 * CIF2MTZ: program to convert mmCIF structure factors (e.g. from PDB)
794 to MTZ (Martyn Winn)
|
795 ccb 1.54 * FSEARCH: program to perform upto 6 dimensional molecular (envelope)
796 replacement search (Q.Hao)
|
797 pjx 1.53 * IAM (UNSUPPORTED): A specialised program for windows
798 purpose of this program is to just return the user name to std out
799 * PROFESSS (formally eleanorinabox): determination of NCS operators from
800 heavy atoms (Kevin Cowtan)
|
801 pjx 1.56 * REFINDEX: reindex dataset maximising correlation with reference dataset
802 (Ian Tickle). In Unsupported as only preliminary version.
803 * REFORIGIN: apply best origin shift to PDB atom co-ords according to
804 reference file (Ian Tickle). In Unsupported as only preliminary version.
|
805 ccb 1.54 * ROTAMER: list amino acids whose side chain torsion angles deviate from
806 Richardson's Penultimate Rotamer Library (Dirk Kostrewa)
807 * SAPI: heavy atom site location (Y.X.Gu, C.D.Zheng, H.F.Fan, Q.Hao)
|
808 pjx 1.53 * STGRID: modified version of STNET, produces a plot for measuring
809 the angular co-ordinates on a stereographic projection (Ian Tickle)
810 * TCL2HTML: Tcl script to convert Tcl script and CCP4i .def files to
811 html, with line numbering, colouring of comments, and html anchors
812 (Liz Potterton)
813
814 * Graphical User Interface:
|
815 pjx 1.56 * Version 1.3.7.
|
816 pjx 1.53 * Prepare HA data: includes option to apply high resolution cutoff
817 for MAD data (Revise RESO keyword). New option to input "native
818 data".
819 * FFT/PATTERSON tasks: upper sigma level now defaults to 100.
|
820 pjx 1.55 * New IMPORT/EDIT PROTEIN SEQUENCE task in Coordinate Utilities.
|
821 pjx 1.53 * MLPHARE task: new option to generate anomalous map. Don't allow
822 centric data only if anomalous difference data is used.
823 * REFMAC5: default for setting up restraints is now "do not check
824 anything".
825 * TRUNCATE: new option to input amplitudes (for analyses only).
826 * Tasks for importing data will now complain if you do not set a
827 project name or dataset name.
828 * Most tasks will get default title if you don't set one. When you
829 see how dull the default is, you will want to set your own.
830 * Selection behaviour for the job list in the main window has
831 changed: only last clicked item is selected. Selecting multiple items
832 is acheived by either ctrl-click (adds to selection) or shift-click
833 (add all items up to previously clicked line). Multiple items can
834 also be selected by clicking and dragging.
835 * Experimental Phasing module: "Merge datasets" task (CAD) added.
836 * MTZ label selection: the maximum length of menus of MTZ file labels is
837 now set in the "Configure Interface" window. Menus which have more than
838 this number of entries will be broken up into multiple columns.
839 * CreateLine command modified to:
840 1) Allow 'packing' of widgets into BLT table; 2) Use a different
841 naming scheme for widgets.
842 pjx 1.53 * Modules and Tasks: the list of modules and tasks is now read from a
843 modules.def file. Entries in an additional modules.def file placed in the
844 user's local area (e.g. $USER/.CCP4/unix/modules) will be appended to those
845 read from that in the main CCP4i area. The modules.def file can
846 be edited using the "Edit Modules File" task under the "System Admin" menu.
847 * Import Scaled Data: new task gives a single interface for importing data
848 from either Scalepack or D*trek - replaces the old Scalepack2mtz and
849 Dtrek2mtz tasks.
850 * OASIS: new task interface for phasing SIR or SAD data.
851 * ANISOANL, TLSANL: new task interfaces.
852 * modules_utils.tcl: new procedures to edit the modules.def files.
853 * Kill Job: modified to recursively kill all subprocesses of the script.
854 * Data Harvesting: the default is now to create harvesting files in the
855 current project directory, for tasks which support harvesting.
856 * PHISTATS: new task interface for phase set analyses.
857 * SFTOOLS: new option to generate Dano from F(+) and F(-).
858 * Main window: default size has been increased, so that all menu items
859 are visible on startup (the user can still resize it)
860 * AddOutputDir: new command to add a directory to the list of output "files"
861 from a job. The directory will not be displayed in the list of output files
862 but will be included in the cleanup procedure if the user deletes the job.
863 pjx 1.53 * SCALA: substantial changes for handling input and output datasets.
864 * CAD: new option to automatically check for and correct inconsistent
865 indexing between input files.
866 * XML: new xml_utils.tcl file contains procedures for handling CCP4 XML
867 files. Matthews and Molrep tasks will use XML to pass information
868 automatically if XML output is specified in preferences. NB these options
869 are developmental only.
870 * ARP/wARP: stand-alone interface has been withdrawn - get the latest ARP/wARP
871 suite and CCP4i interface from http://www.arp-warp.org/
872 * Mail CCP4: on Windows systems now calls up the CCP4 on-line help.
873 * Install New Task: substantially revised version allows install, uninstall and
874 export of new tasks. See documentation for full details.
875 * MAPCUTTING: new interface from Kevin Cowtan.
|
876 ccb 1.54 * DM: can specify NCS operators in a number of different ways (euler angles,
877 polar angle, rotation matrix or O matrix).
|
878 pjx 1.55 * WHATCHECK: new interface (Maria Turkenburg/Peter Briggs).
|
879 pjx 1.56 * File Viewers: user can set their default PDB and map viewer in Preferences.
880 * ROTAMER: new interface.
|
881 pjx 1.53
882 * Documentation:
883 * STNET: updated to clarify usage.
884 * CCP4i: extensive new documentation for all core Tcl routines.
885
886 * Withdrawal:
887
888 *
889
890 * Examples
|
891 pjx 1.56 * toxd.mtz, rnase18.mtz and rnase25.mtz now distributed as well as .na4 files.
|
892 pjx 1.53
|
893 pjx 1.48 Summary of significant changes to CCP4 at version 4.1
894 ------------------------------------------------------
895
896 * Building etc.:
897 * ccp4.setup: shouldn't add duplicated entries to the PATH variable.
898 * cif_mmdic.lib (binary version of mmCIF dictionary) now installed
899 in $CLIB rather than $CLIBD.
|
900 pjx 1.50 * configure: (i) updated for OSF1 V5.0. (ii) Always builds fsplit
901 automatically in bindir (defaults to $CBIN) and uses this in the build.
902 (iii) Use --with-lapack option to include LAPACK maths libraries in
903 build (see MODLIB documentation).
|
904 pjx 1.48
905 * Program changes:
906 * AMORE: sorts rotation function output for improved solutions.
|
907 ccb 1.52 * AREAIMOL: TRANS keyword - search extended from +/-1 lattice vectors to
908 +/2 vectors
|
909 pjx 1.48 * AXISSEARCH: updated output; now uses keyworded input
910 (see documentation).
911 * CAD: new keywords DCELL and DWAVELENGTH for adding/changing dataset cell
912 and wavelength attributes.
913 Applies temperature factor as part of scaling (via SCALE keyword).
914 * DM: version 2.1. Major changes are: NCS operators are now output as
915 Euler angles plus translations; program will calculate the value of
916 NMER automatically if it is omitted by the user; XtalView/O files
917 can be output to visualise the NCS elements.
|
918 ccb 1.52 * DYNDOM: no longer sensitive to the order of the atoms in the PDB file.
|
919 pjx 1.50 * F2MTZ: added summary tags to output.
|
920 pjx 1.48 * GENSYM: new keywords SORT (specifies order output for sites) and
921 CHAIN (assigns chain ids).
922 * GEOMCALC: prints out equations of fitted planes.
923 * IPDISP: revised version of ipdisp script; new spdfil for PX210
924 detector.
925 * MAPMASK: new XYZLIM MATCH option takes the output map limits from
926 a map supplied by the user.
927 * MAPROT: changes to CELL, GRID and SYMMETRY keywords (now have
928 WORK/XTAL subkeys), to AVERAGE keyword (change to format for entering
929 NCS operators) and new INVERT keyword. Option to cut density from
930 one map and transfer to another.
931 * MLPHARE: fixed DCYCLE REFCYCL option (was broken); substantial
932 reformatting of logfile output.
933 * PDBSET: new NOISE option adds random shifts to selected atom
934 coordinates. Checks that symmetry from SPACEGROUP is consistent
935 with that from input PDB file. Calculates fractional, as well as
936 orthogonal limits on coordinate set. New suboption FILE for
937 TRANSFORM keyword (see documentation). Chain selections now use
938 ChainId, if SegId is blank then SegId is always set to ChainID on
939 output.
940 * PEAKMAX: change of defaults, residue type for output set to HOH,
941 pjx 1.48 default atom name to O.
|
942 pjx 1.50 * PHISTATS: new SHIFT keyword applies a fractional shift to the second
943 phase set - useful if two phase sets refer to different crystal
944 origins.
945 * PROTIN: now can apply restraints from one residue to (a
946 symmetry-related copy of) itself.
|
947 pjx 1.48 * REBATCH: new CELL/WAVELENGTH keywords.
948 * REINDEX: new (optional) subkeywords HKL/AXIS for REINDEX keyword,
949 control how the transformations are supplied to the program.
|
950 ccb 1.52 * REVISE: new RESO keyword to set maximum resolution.
|
951 pjx 1.48 * RSPS: new version 4.2 from Stefan Knight.
|
952 pjx 1.50 * SCALA: new version 2.7.5.
|
953 pjx 1.48 * SCALEPACK2MTZ: added summary tags to output.
954 * SORTMTZ: change of defaults, residue type changed to HOH, atom
955 to O.
956 * TLSANL: many changes associated with new TLS option of refmac.
957
958 * Library:
959 * CCPLIB: CCPVRS prints 15 characters from program name (was 10).
960 CCPFYP recognises new command-line arguments -nohtml (suppress
961 output of html tags) and -nosummary (suppress output of summary
962 tags).
963 * FFFEAR_fraglib: library of representative protein fragments for FFFEAR.
964 * KEYPARSE: new entry ParseAtomSelect supports simple atom selection
965 commands.
966 * LAPACK: source code for BLAS and LAPACK packages included from
967 Netlib.
968 * MTZLIB: new DCELL and DWAVEL records in MTZ header for dataset-specific
969 cells and wavelengths. New routines LRIDC and LWIDC for read/write
970 dataset cell and wavelength info.
971 * MODLIB: a number of routines have been added to the library from
972 various programs - see the MODLIB documentation.
973 * PARSER: new routine RDATOMSELECT supports simple atom selection
974 pjx 1.48 commands.
975 * RWBROOK: s/r XYZOPEN checks for consistency between PDB defn.s of
976 symmetry operations (taken from REMARK 290 lines, if present) and the
|
977 pjx 1.49 order in $CLIBD/symop.lib or mtzlib. s/r SFREAD2 now correctly reads
978 form factors for one character atom names from atomsf.lib (S, I and B
979 were affected) (Clemens Vonrhein).
|
980 pjx 1.48 * SYMLIB: s/r SYMFR2 now recognises real- and reciprocal-space
|
981 ccb 1.52 axis vector operations, e.g. a*+c*,c*,-b*; new s/r SETLIM_ARP
982 returns the ARP asu limits.
|
983 pjx 1.48 * SYMOP.LIB: fixed point groups for alternate spacegroups 1003, 1004,
984 1005, 2005, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015.
|
985 pjx 1.51 * XDL_VIEW: new version 4.4
|
986 pjx 1.48
987 * New programs:
988 * ANISOANL: various analyses of model anisotropic U values (Martyn Winn)
989 * ccp4keys: awk script for extracting keywords form a log file in a format
990 which can be cut and pasted into a new command file. (Kevin Cowtan)
991 * CAVENV: Calculates cavities in macromolecular structures (Anne Volbeda)
992 * CCP4MAPWISH: customised wish interpreter required for MAPSLICER. (Peter Briggs)
993 * COMBAT: replacement for ROTAPREP. (Alun Ashton)
994 * DTREK2MTZ: converts d*trek scalemerge output into MTZ format. (Jim Pflugrath)
995 * FFFEAR 1.2: Fast Fourier FEAture Recognition program. (Kevin Cowtan)
996 * FFJOIN: joins together fragments from FFFEAR. (Kevin Cowtan)
997 * MAP2FS: jiffy to convert CCP4 maps/masks to XtalView fsfour format. (Kevin Cowtan)
998 * MAPSLICER: viewer for contoured sections through CCP4 maps. (Peter Briggs)
999 * MOSFLM: now distributed with CCP4. (Andrew Leslie / Harry Powell)
1000 * REFMAC5: major new version of REFMAC (Garib Murshudov). Old refmac and
1001 protin moved to unsupported.
1002 * ROTGEN: Simulate X-ray diffraction rotation images. (John Campbell)
|
1003 pjx 1.51
1004 * Graphical User Interface:
1005 * Installation: CCP4i no longer requires Tcl/Tk to be built with a non-default
1006 flag. It is best run using the bltwish interpreter.
1007 * Monomer Library Sketcher: for graphics display of monomers, and
1008 interface to Libcheck and the monomer geometry libraries.
1009 * New interfaces to BAVERAGE, CONTACT, FFFEAR, DMMULTI,
1010 DTREK2MTZ, SFTOOLS for SF analysis, SIGMAA, and WATERTIDY.
|
1011 pjx 1.48
1012 * Documentation:
1013 * alternate_origins: lists alternate origins for different spacegroups.
1014 * lsqkab.html: added a "known problems" section.
1015 * symlib.html: extended section on applying symmetry operations.
1016
1017 * Withdrawal:
1018
1019 * ROTAPREP: moved to unsupported.
1020
1021 * Examples
1022 * axissearch.exam: updated for revised version of AXISSEARCH.
1023 * toxd.pdb: waters renamed to HOH O1.
|
1024 pjx 1.49 * run-all: testing script in $CEXAM/unix/runnable which will
1025 run all examples and report any failures
|
1026 pjx 1.48 * tutorial2000: ccp4i-based tutorials. Old tutorials removed since
1027 getting out of date.
1028
|
1029 mdw 1.44 Summary of significant changes to CCP4 at version 4.0
1030 ------------------------------------------------------
1031
1032 * Building etc.:
|
1033 mdw 1.47 * configure: new options --help, --with-rxdispencer and --disable-ccif
1034 New system linux_compaq_compilers
|
1035 mdw 1.44 * etc/GFAC2PDB.COM added for VMS
1036 * include/ccp4.setup-dist and ccp4.setup-bash: CCP4_OPEN set to
1037 UNKNOWN by default since necessary for some programs, and this
1038 is common practice. Beware over-writing existing files!
|
1039 mdw 1.46 * lib/data: running fontpack has been moved to "make install" step,
1040 since if a shared library is used it needs it to have been installed.
|
1041 mdw 1.44
1042 * Program changes:
|
1043 mdw 1.46 * AMORE: major new version from Jorge Navaza
|
1044 mdw 1.44 * AREAIMOL: default MODE is now NOHOH. Attempts to identify isolated
1045 areas of surface (eg cavities) in MODEs NOHOH and ALL.
1046 * ARP_WARP: ARP/wARP v5.0 - replaces "arpp".
1047 * CONTACT: broken MODE ISUB fixed. CRYST1/SCALE cards not required except
1048 for MODEs AUTO and IMOL. New keyword BIGSEARCH allows larger volume to
1049 be searched for contacts under MODE AUTO. Should correctly identify H32
1050 and R32.
|
1051 mdw 1.47 * COORDCONV: extended to read *.ha format files.
|
1052 mdw 1.44 * DETWIN: LABIN keyword added - program now accepts F's and I(+/-).
1053 Performs new tests for twinning as a function of twinning fraction and
1054 resolution - see documentation. OPERATOR keyword replaces existing
1055 SYMMETRY keyword (which is still valid).
|
1056 mdw 1.46 * DM: version 2.0.5.
|
1057 pjx 1.48 * FHSCAL: can now apply scales calculated for F's to F(+), F(-), Imean,
1058 I(+) and I(-), and warns if not all scalable members of a dataset have
1059 scales applied. AUTO option enables automatic selection of all
1060 scalable columns in chosen datasets.
|
1061 mdw 1.44 * IPDISP: new version and new spdfils for reading packed MAR image files.
1062 * MAPDUMP: accepts END/RUN/GO keyword as well as end-of-file.
1063 * MLPHARE: keyword COORDS writes heavy atom coordinates to pseudo-pdb file.
1064 * MTZ2VARIOUS: Extra LABIN columns FPART_BULK_S and PHIPART_BULK_S for
1065 CIF output.
1066 * MTZMADMOD: labels changed so that +/- are now (+)/(-)
1067 * NCSMASK: new SPACING subkeyword for GRID option, to set arbitrary grid
1068 spacing.
1069 * PDBSET: added OCCUPANCY RESET and EXCLUDE SIDE options. Fixed broken
|
1070 mdw 1.47 TRANSFORM FRACTIONAL option. New EXCLUDE WAT/HOH option.
|
1071 mdw 1.44 * PREPFORM, PREPSHEL: new version as part of ARP/wARP suite v5.0.
1072 * PROTIN: redimensioned for ARP/wARP.
1073 * RWCONTENTS: keyword NHOH added to estimate no. of water molecules
1074 that can be found by PX (Carugo and Bordo).
1075 * REBATCH: A new sub keyword to BATCH, MAXWIDTH, has been added to specify
1076 the maximum width of reflections. Those with higher widths are rejected.
|
1077 mdw 1.47 * SCALA: new version 2.7.2.
|
1078 mdw 1.44 * SCALEIT: can now apply scales calculated for F's to F(+), F(-), Imean,
1079 I(+) and I(-), and warns if not all scalable members of a dataset have
|
1080 mdw 1.47 scales applied. AUTO option enables automatic selection of all
1081 scalable columns in chosen datasets.
|
1082 mdw 1.44 * SCALEPACK2MTZ: Added code to insert html tags in log files.
1083 * SFCHECK: version 5.3.4
1084 * SORTMTZ: Added code to insert html tags in log files.
1085 * SURFACE: prints out total accessible area after each calculation.
1086 * TLSANL: New keyword BINPUT to specify whether Bs or Us in XYZIN.
1087 * TOPP: topp.f, autosnd.f, toplist.f - all leading tabs changed to spaces
1088 for compilation on AIX. Now version 6.5
1089 * TRUNCATE: new loggraph table of centric and acentric moments for identifying
1090 twinning. Plots of F/sigma added to falloff plots for identifying anisotropy.
1091 Code added to check if data is anisotropic. Included a new keyword SCALE that
1092 when provided overrides the wilson plot scale. Added code to insert html tags
1093 in log files.
1094 * WATERTIDY: fixed faulty oxygen atom recognition.
1095 * WATNCS: all leading tabs changed to spaces for compilation on AIX.
1096
1097 * Library:
1098 * lib/ccif: Peter Keller's ccif library for handling mmCIF
1099 * cciflib.f: new library for handling mmCIF coordinate files. At present,
1100 not used by distributed programs. Uses libccif.a
1101 * harvlib.f: new library for writing data harvesting files. Used by
1102 MLPHARE, TRUNCATE and RESTRAIN. Uses libccif.a
1103 mdw 1.44 * lgglib.f: all leading tabs changed to spaces for compilation on AIX.
1104 * rwbrook.f: new routine NUM_EXPECTED_WATERS. Changes to XYZOPEN (issues
1105 warnings if no CRYST1 or SCALE cards are found in input PDB file).
|
1106 mdw 1.45 * sc_radii.lib: atomic radii library file for new SC program.
1107 * symlib.f: new s/r CALC_ORIG_PS.
1108 * symop.lib: one line per symmetry operation. Some minor corrections.
|
1109 mdw 1.44
1110 * New programs:
1111 * MOLREP: automated program for molecular replacement, from Alexei Vagin
1112 * OASIS: program for breaking phase ambiguity in OAS or SIR, from Quan Hao
1113 * RWCONTENTS: promoted from unsupported.
1114 * SC: program to analyse shape complementarity of molecular interfaces
1115 * T_SHIFT: part of ARP/wARP suite v5.0.
1116
1117 * Documentation:
|
1118 mdw 1.46 * ccplib.html: new documentation for the CCP4 utility routines in CCPLIB.
1119 * diskio.html: new documentation for the I/O library routines in DISKIO.
|
1120 mdw 1.44 * INDEX.html: new File Formats section. Includes pdbformat.html taken
1121 from original rwbrook.html, and mmcifformat.html for mmCIF and CCIF.
1122 Descriptions of MTZ and map formats can be found in Library section.
|
1123 mdw 1.46 * keyparse.html: new documentation for the KEYPARSE library routines.
1124 * library.html: new documentation for the routines in LIBRARY.C.
|
1125 mdw 1.44 * makedict.html: now has hints for making PROTIN dictionary entries.
1126 * modlib.html : new documentation for the CCP4 maths routines library
1127 MODLIB.
|
1128 mdw 1.46 * parser.html: new documentation for the PARSER library routines.
1129 * unix.html: documentation for the library routines in UNIX.M4, VMS.FOR and
1130 W32MVS.
|
1131 mdw 1.44
1132 * Withdrawal:
1133
1134
1135 * Examples
1136 * arp_warp.exam: updated version of old "arpp.exam" using ARP/wARP v5.0
|
1137 mdw 1.46 * cad_rnase.exam: example using CAD to add project and dataset
1138 information to an mtz file.
|
1139 mdw 1.44 * makedict.exam: two examples of using MAKEDICT.
|
1140 mdw 1.46 * mtzMADmod.exam: example of adding F+/- columns to a file.
|
1141 mdw 1.44 * oasis_oas.exam, oasis_sir.exam: two examples for OASIS.
1142 * protin_substrate: updated to use MAKEDICT.
1143 * rebatch.exam: A new example using the aucn data.
1144 * rnase.pdb: terminal oxygens renamed from "OE" to "OXT",
1145 in line with the PDB standard.
|
1146 mdw 1.45 * sc.exam: two non-runnable examples for SC.
|
1147 mdw 1.46 * sfall.exam: three simple examples of running SFALL.
1148 * surface_rnase.exam: example of running SURFACE on rnase data.
|
1149 mdw 1.44 * toxd.pdb: terminal oxygen renamed from "OE" to "OXT",
1150 in line with the PDB standard.
1151
|
1152 mdw 1.40 Summary of significant changes to CCP4 at version 3.5
1153 ------------------------------------------------------
1154
1155 * Building etc.:
1156 ** configure script has new system irix64 for 64 bit compilation on
1157 SGI with irix 6.*
1158 ** configure script has new option --with-x for sgi/linux/and osf1
1159 will compile the xwindows progs
1160 ** ccp4.setup-dist/bash : has PLOT_COMMAND and PRINT_COMMAND that need
1161 to be set for XCCPJIFFY's to work correctly.
1162 * duptree: new version using relative pathnames. Original behaviour can
1163 be obtained by using the -a (absolute pathname) flag.
1164 * Makefile.in in $CCP4 has new JAVATARGETS target, currently only used
1165 for moving java executables JLogGraph.class and JLogCanvas.class from
1166 $CPROG to $CBIN upon "make install".
1167 * x-windows/XCCPJIFFY: added IRIX_6 option (actually the same as IRIX_5
1168 but clearer to have it explicit)
1169 Irix 6.5 needed a section to itself.
1170 ** x-windows/XCCPJIFFY: added Imakefile.in
1171
1172
1173 mdw 1.40 * Program changes:
1174 * AREAIMOL: substantially updated version now also incorporates DIFFAREA,
1175 RESAREA and WATERAREA. See documentation.
1176 * CAD: new keywords PNAME/DNAME for adding dataset info. Will now swap
1177 F+/F- or I+/I- columns on changing hand of indices.
1178 * CONTACT: substantially new version.
1179 * DM: Version 2.0.3
1180 Output log file enhanced if viewed through web browser.
1181 * ECALC: now uses absolute differences to calculate E. EXCLUDE keyword
1182 added. Extra column SIGE written to output mtz. Scatter Plot removed
1183 from the log as the info is already in the tables.
1184 * FFT,FFTBIG: XYZLIM ASU option automatically sets map limits to correct
1185 asymmetric unit.
|
1186 mdw 1.43 * FHSCAL: Modification from Richard Kingston to process F+/- columns.
|
1187 mdw 1.40 * FREERFLAG: New keyword SEED to seed random number generator using
1188 current time. Systematic absences also assigned a FreeR flag (no longer
1189 flagged as missing). OLDFREE keyword removed.
1190 * HKLVIEW: new -d option specifies resolution limit.
1191 * ICOEFL: LABOUT and END keywords fixed.
1192 * IPDISP: extra spdfil files added for new detectors. Some options
1193 for existing detectors updated.
1194 * MAPMASK: SYMM now over-rides map file header. Optional MODE keyword
1195 added.
1196 * MTZ2VARIOUS: OUTPUT CIF now gives correct spacegroup format. OUTPUT
1197 CNS and OUTPUT SCAL (for SOLVE) added.
1198 * MTZDUMP: limits output in "resolution" column have been corrected.
1199 * NPO: subkeyword FRAC added to existing SECTNS keyword.
|
1200 mdw 1.43 * PDBSET: SPACEGROUP and EXCLUDE HEADER options fixed.
|
1201 mdw 1.40 * PEAKMAX: New output option FRAC added. Existing output PEAKS option now
1202 writes to logical name PEAKS. Program now outputs the height/rms(density)
1203 (instead of height) in output files and in logfile. Some formats changed
1204 in logfile and OUTPUT BROOKHAVEN.
1205 * PROTIN: fixed problems with being unable to assign a SPECial distance
1206 between atoms in multiple confirmations, and with checks only for
1207 distances being applied for first residue of non-protein chains.
1208 * REFMAC: version 4.0.2 with anisotropic refinement
1209 * REINDEX: new version - see documentation.
1210 * ROTAPREP: option SCAL_NM2 for new SCALEPACK output.
1211 * RSTATS: functionality of RESOLUTION keyword changed. All reflections
1212 now written to output mtz.
1213 * RWCONTENTS: extended to give estimates of the fraction of the unit cell
1214 which is empty or which contains solvent. Also calculates Matthews
1215 coefficient.
1216 * SCALA: new version 2.5.5.
|
1217 mdw 1.41 Output log file enhanced if viewed through web browser.
|
1218 mdw 1.40 * SCALEIT: SCAT keyword to include scatter plots in log files. Default
1219 is now not to.
1220 * WILSON: can read in intensities or amplitudes.
1221
1222 * Library:
1223 * lgglib.f: routines from Guoguang Lu
1224 * libhtml.f: new library routines for adding HTML tags into program output
1225 so that log files can be viewed as HTML documents. Associated java code in
1226 JLogGraph.java (compiled as JLogGraph.class and JLogCanvas.class) allow
1227 log graphs to be embedded and viewed directly through Java-enabled HTML
1228 browser.
1229 * library.c: new routine hgetlimits for harvesting
1230 * maplib.f: descriptive names for subroutines now available alongside existing
1231 subroutine names. New routines CCP4MAPHEAD, CCP4MAPIN and CCP4MAPOUT added.
1232 * modlib.f: new matrix multiplication routines MATMULNM and MATMULGEN.
1233 * protin.dic: IUM residue entry revised with more comprehensive list of elements.
1234 * rwbrook.f: routines XYZADVANCE and WBCELL now print spacegroup name (if available)
1235 after cell info of CRYST1 card. New routine WBSPGRP used to set spacegroup name.
|
1236 mdw 1.43 RBSPGRP now returns spacegroup name automatically left-justified. New routine
1237 RWNOHEAD suppresses output of CRYST1 and SCALE cards.
|
1238 mdw 1.40 * symop.lib: extended version of symop.lib, containing additional alternative
1239 spacegroup names. Groups 1017, 2017, 2018, 3018 added. (Old symop.lib
1240 retained in symop_old.lib)
1241 * symlib.f: new routine MSYMLB2 to return CIF-style spacegroup name. New routine
1242 MSYMLB3 returns most detailed spacegroup name, checks all symmetry operators
1243 in spacegroup form a closed set, and derives the pointgroup from the existing
1244 subroutine PGDEFN (ignoring that given in $SYMOP). New routine SYMTR4 converts
1245 matrices to symmetry operations more consistently than existing SYMTR3.
1246 Routines SETUP, LOOKUP and ZEROIT renamed (now preceeded by "CCP4_HASH_"), and
1247 relevant programs altered (POSTREF, REBATCH, SCALA).
1248 * $CLIBD/protin.dic: HOH added as residue to fit pdb format
1249
1250 * New programs:
|
1251 mdw 1.42 * DETWIN: detwins merohedrally twinned data.
|
1252 mdw 1.40 * DYNDOM: Program to Determine Domains, Hinge Axes and Hinge Bending Residues
1253 in Proteins where Two Conformations are Available. From Steve Hayward.
1254 * FINDNCS: detect NCS operations automatically from heavy atom sites.
1255 From Guoguang Lu.
1256 * MTZMADMOD: Jiffy for converting between F+/F- and F/D
1257 * TOPP: an automatic topological and atomic comparison program for protein
1258 structures. From Guoguang Lu.
1259 * WATNCS: Pick waters which follow NCS and sort out to NCS asymmetric unit.
1260 From Guoguang Lu.
1261
1262 * Documentation:
1263 * ipdisp.html: contains list of available spdfils and new section on creating
1264 and custominsing spdfils.
1265 * libhtml.html: documentation for new libhtml.f library subroutines.
1266 * protin.html: contains example with RNA.
1267 * symlib.html: documentation for symmetry library subroutines in symlib.f.
1268 * freerunique.html, reindexing.html, scalechoose.html, twinning.html: new
1269 general documentation.
1270
1271 * Withdrawal:
1272 * DIFFAREA, RESAREA and WATERAREA all now incorporated into AREAIMOL.
1273 mdw 1.40
1274 * Examples
1275 * areaimol.exam: examples for new version.
1276 * toxd.pdb: Chain names added and TER card at end of protein
1277 * ncsmask.exam: one run of pdbset removed as toxd.pdb now has chain ID
1278 * arpp.exam: pdbset run ajusted. extend replaced with mapmask.
1279 * watpeak.exam: pdbset run ajusted.
1280 * watertidy-3shells: pdbset run ajusted.
1281 * sortwater.exam: pdbset run removed.
1282 * bplot.exam: resudue names changed to include CHAIN ID.
1283 * f2mtz.exam: adjusted XPLOR example to accept output from new mtz2various.
1284 new example added.
1285 * mtz2various.exam: extra example of OUTPUT USER with DUM labels.
1286 ** rnase : $CEXAM/rnase/ directory added with data/scripts/pdb
1287 see $CEXAM/rnase/README for details
1288
1289
|
1290 mdw 1.38 Summary of significant changes to CCP4 at version 3.4
1291 ------------------------------------------------------
1292
1293 * Building etc.:
1294 * duptree: new script for setting up multiple installations
1295 * C programs: changes to PLTDEV, BINSORT and SOLOMON so that they should
1296 compile on HPUX.
1297 * linux/g77: all programs should now compile with linux/g77
|
1298 awa 1.39 * x-windows: trial configure and Makefile.in for IRIX, OSF1 and LINUX.
|
1299 mdw 1.38
1300 * Program changes:
1301 * AREAIMOL: now takes keyworded input.
1302 * FFT/FFTBIG: will now print out Harker sections.
|
1303 awa 1.39 * GETAX: New version - g77 compliant.
|
1304 mdw 1.38 * NPO: now can take XYZIN again! New version from Eleanor Dodson.
|
1305 awa 1.39 * PROCHECK: New version - now g77 friendly.
|
1306 mdw 1.38 * SCALA: version 2.4.2 included
1307 * SIGMAA: subsubkeywords LOW and HIGH of COMB RESO removed, since
1308 of little use and didn't work properly.
1309 * SORTWATER: Duplicate waters (after applying symmetry operators) are removed.
1310 * TRUNCATE: FALLOFF option to visualise anisotropy (Yorgo Modis).
1311 * VECTORS: now sets Bfactors to 1.0 to fit in with NPO
1312
1313 * Library:
1314 * ccplib: minor y2k fixes.
1315 * rwbrook: new routines RBRORF2, CVANISOU, RBSPGRP.
1316 * symlib: changes to SYMTR3 to allow calculation of Harker sections,
1317 new ENTRY CENTPHS to return PHASE class.
1318
1319 * New programs:
1320 * BAVERAGE: promoted from Unsupported (now keyworded).
1321 * BPLOT: promoted from Unsupported.
1322 * MAPDUMP: from old unsupported PRMAP.
1323 * RANTAN: Direct Method module for the determination of heavy atom positions
1324 in a macro-molecule structure or to determine a small molecule structure.
1325 * SFCHECK: Structure factor checking
1326 * SFTOOLS: Reflection data file utility program from Bart Hazes.
1327 mdw 1.38 * DMMULTI: multi-xtal density modification package
1328
1329 * Documentation:
1330 * html versions of dm_ncs_averaging and dm_skeletonisation added.
1331 * arppdoc.ps removed - contents included in arpp.html
1332 * $CCP4/manual/procheck/manual.ps removed since out-of-date. New
1333 comprehensive html version.
1334
1335 * Withdrawal:
1336 * ABSCALE: obsolete
1337 * AGROVATA/ROTAVATA: replaced by SCALA
1338 * ENVELOPE: replaced by DM
1339 * EXTEND: moved to unsupported, replaced by MAPMASK.
1340 * FLATMAP: replaced by DM
1341 * PROLSQ: replaced by REFMAC
1342 * PSAVER: replaced by NCSMASK/DM.
1343 * RESLICE: replaced by MAPMASK.
1344
1345
|
1346 mdw 1.37 Summary of significant changes to CCP4 at version 3.3
1347 ------------------------------------------------------
1348
1349 * Building etc.:
1350 * $CCP4/Makefile.in: makeman script automatically runs when typing make
1351 from $CCP4.
1352 * $CHTML/makeman.csh: man pages can effectively be generated by running
1353 this script. Symbolic links are made from $CCP4/man/cat1/ to the $CDOC
1354 files which are then viewable by `man`.
1355 ** $CINCL/ccp4.setup: $CMAN has been removed and $CHTML = $CCP4/html has been
1356 added. $CCP4_BROWSER added - it is to be the path and name of an html browser
1357 to be used for viewing ccp4 documentation. ccp4help alias added to run
1358 $CCP4_BROWSER with file $CHTML/INDEX.html
1359 * MAKEFILE.COM: "DEC Fortran" is no longer a valid test between Alpha and
1360 VAX. Test has been changed.
1361 * MAKEFILE.MMS: has been removed as it was out of date. Nobody noticed so
1362 perhaps everyone is using the makefile.
1363 * MOSFLMBITS.COM: has been removed because it is no longer needed.
1364 * configure: changed building of shared library for OSF1. Also, `pwd`
1365 changed to `pwd`/ as there may have been problems installing the shared
1366 library. The -with-mosflm option is being removed. The library routines
1367 mdw 1.37 are not need for the new version of MOSFLM. --tmpdir=DIR option added.
1368 g77 is now the default compiler for linux - not fully tested.
1369
1370 * Program changes:
1371 * AGROVATA: program labels changed from I+ to I(+) etc. to be consistent
1372 with SCALA and TRUNCATE.
1373 * BONES2PDB: now recognises BONES_ATOM_XYZ and BONE_ATOM_XYZ as valid
1374 datablock headers, as well as SKEL_ATOM_XYZ.
1375 * CROSSEC: input now fully keyworded.
1376 * * DM: have version 1.8.1 from Kevin. The 'solvent flipping' option has been
1377 removed and solvent flattening and histogram matching are compulsory.
1378 * ECALC: now has an option "SNB" which outputs E's in the format
1379 Shake-and-Bake reads.
1380 * FFT: P222 and P2221 have been removed as valid FFTSPACEGROUPs becuase of
1381 errors in calculating the maps. The C222 (21) routines are now working
1382 properly.
1383 * FFT,FFTBIG: there was a chance that F could be negative if bias removed.
1384 Fixed so that F > 0. ABCOEFFS file altered to avoid mis-interpretation.
1385 * FHSCAL: now has an option "CENT" which uses only centrics for scaling,
1386 which may be more accurate in space groups with a lot of centrics such
1387 as tetragonal
1388 mdw 1.37 * HKLVIEW: changes to handle MNFs. Partials were not added properly, now
1389 fixed.
1390 * MAMA2CCP4: automatic format identification didn't work for VMS. Fixed.
1391 * MLPHARE: format error when using 'PRINT RMSF RMSE' fixed. Problem with
1392 FOM out of range 1.0 - 0.0 fixed. New APPLY keyword for applying
1393 refined scales to derivative data. Maximum number of derivatives
1394 increased to 20. Reflections could have been rejected incorrectly if
1395 data was anomalous but had no deltaF. Now fixed.
1396 * MTZ2VARIOUS: new option INCLUDE FREER to select just freer set.
1397 If FREE column included and not used in INCLUDE/EXCLUDE options, then
1398 OUTPUT TNT will now output it.
1399 * MTZDUMP: new HEADER keyword, with corresponding -e option to mtzdmp.
1400 * * NCSMASK: problem with keyword 'OVER' removed.
1401 * * NPO: fixed one bug with USEORTEP. Probably others. FILE keyword removed
1402 now must assign coordinate input to XYZIN1, XYZIN2 ...
1403 * OVERLAPMAP: END keyword added, error in xloggraph output removed.
1404 * PROTIN: New CONTACTS subkeywords for extended anti-bumping checking.
1405 New SPECIAL SYMM and CHNTYP SPECIAL RESN <> TO <> keywords.
1406 * POSTREF: keyword ABSORPTION replaced with INSCALE
1407 * REBATCH: DETECTOR option added, for use with SCALA. Added BATCH [ALL] option.
1408 * * RESTRAIN: New Version 4.5 added.
1409 mdw 1.37 * ROTAPREP: an extra input option has been added MTZI. Also, new keyword
1410 DETECTOR has been added for use with SCALA. It now also outputs MNFs in
1411 columns which are not appropriate (eg XDET, YDET). CELL keyword will
1412 override the cell read in from DENZO or MTZ formats.
1413 * * ROTAVATA: program labels changed from I+ to I(+) etc. to be consistent
1414 with other programs.
1415 * * SCALA: new version 2.3.1 from PRE. Has made AGROVATA and ROTAVATA
1416 obsolete.
1417 * SCALEPACK2MTZ: output labels changed from I- to I(-) etc. to avoid
1418 problems with parser. Missing data treatment added. New keywords
1419 ANOM and CELL.
1420 * SCALEIT: checks on keyword combinations of ANALYSE, SCALE and REFINE
1421 now applied. Anisotropic scale was not applied when using SCALE. Also, if
1422 SCALE card used then the scales specified are not refined.
1423 * SFALL: checks to see if symmetry assigned (not all options have HKLIN).
1424 * SIGMAA, TRUNCATE, WILSON: typo found in the subroutine LSQ. Effects the
1425 fitting of the straight line through the Wilson PLot.
1426 * SOLOMON: can now read various O mask formats, can decide automatically
1427 which. However, will only output CCP4 masks.
1428 * SORTWATER: corrected syntax of NCS ... SAME command
1429 * SURFACE: FORMAT BNL renamed PDB.
1430 mdw 1.37 * * TRUNCATE: input columns IW(+) etc. now not used (scalepack2mtz doesn't
1431 produce them). Corrections to MNF handling. Input labels now I(-)
1432 instead of I- etc. ANOM OFF now works. It has been changed to use form
1433 factors from atomsf.lib rather than an internal table. This means that
1434 more atom types can be catered for. The values are different from before
1435 so there will be slight differences from earlier version of truncate.
1436
1437 * Library:
1438 * MTZLIB: there was an inconsistency between program labels being case
1439 insensitive and file labels being case sensitive. Now both are case
1440 sensitive. WARNING; program labels must be in upper case when specified
1441 in LABIN.
1442 * RWBROOK: these routines have been changed extensively because of the
1443 proposed change in format for co-ordinate files. This should be
1444 transparent to users (although some programs have been altered, check
1445 documenation) but developers will need to conform to the new routines.
1446 More details can be seen on the Web in the Developers Section.
1447
1448 * New programs:
1449 * ARPP: AUTOMATED REFINEMENT PROGRAM from VICTOR S. LAMZIN.
1450 Note that "arp" has been renamed "arpp" to avoid conflict with unix command.
1451 mdw 1.37 * GETAX from Clemens Vonrhein. Real space searching for rotation axis of
1452 a D<n> or C<n> multimer (<n> = 2,3,4,5,6,...).
1453 * OMIT from Bauke Dijkstra and Fred Vellieux. Calculate omit maps
1454 according to procedure of Bhat.
1455 * RDENT: create dictionary entries for Restrain from PDB file.
1456 * STNET moved from unsupported
1457 * REVISE: program to generate normalised anomlous scattering factor
1458 magnitudes from MAD data (Yao Jia-xing).
1459 * wulff.ps added to 'aggregated' stuff, for generating Wulff
1460 net (Ian Clifton).
1461
1462 * Documentation:
1463 * All program documentation has been converted to html. These are now the
1464 master copies and the plain text docs are generated from them. Man pages are
1465 formally dead. If you set up a cat1 directory pointing to $CDOC then you can
1466 continue to use the man command. A "whatis" file is distributed in
1467 $CHTML so that you can still use man -k or apropos.
1468 * $CCP4/man and $CCP4/unsupported/man have been removed.
1469 All files are now in $CDOC and $CHTML.
1470 * $CHTML/matthews_coef: unforunately the initial formula for Vp was
1471 incorrect and has now been corrected.
1472 mdw 1.37 * Some new flow charts added to manual.
1473
1474 * Examples:
1475 * $CEXAM/unix/runnable/scalepack2mtz.exam added.
1476 * $CEXAM/unix/runnable/agrovata.exam and $CEXAM/unix/runnable/rotavata.exam
1477 removed. If you need an example, you should be using scala.
1478 * $CEXAM/tutorial: the MTZ files which are part of the tutorial are now
1479 distributed as NA4 files. Problem with file names in MR tutorial fixed.
1480 * All *.sh have been converted to *.exam files because of the problems with
1481 viewing these with netscape.
1482
1483 * Withdrawal:
1484 * $CETC/cman: this utility has been withdrawn, as the man pages are now dead.
1485 * $CLIBS/chelp.c and $CLIBS/graflib.f will be moved to the 'mosflm-bits'
1486 directory on the anonymous ftp server. They are not required for the new
1487 version of MOSFLM.
1488 * ABSCALE: moved to unsupported directory.
1489 * AGROVATA: moved to unsupported directory. Function has been taken over
1490 by SCALA.
1491 * PLANES: was unsupported, now withdrawn. Functionality is covered
1492 by GEOMCALC. PLANES hasn't been converted to use new RWBROOK subroutines,
1493 mdw 1.37 but if you want the code to hack, call us at DL.
1494 * POSTREF: moved to unsupported directory.
1495 * PROLSQ: moved to unsupported directory. Use REFMAC.
1496 * ROTAVATA: moved to unsupported directory. Function has been taken over
1497 by SCALA.
1498 * SUPERPOSE: function duplicated in both LSQKAB and POLYPOSE.
1499 * DERIV : was unsupported, functions duplicated in SFALL.
1500
|
1501 acr 1.36 Summary of significant changes to CCP4 at version 3.2
1502 ------------------------------------------------------
1503
1504 * Building etc.:
1505 * $CCP4/x-windows/XCCPJIFFY/Imakefile: compiler options for HPUX sent
1506 by Morten Kjeldgaard.
1507 * $CCP4/x-windows/xdlgjk/Makefile: added install and empty-targets
1508 procedures, in line with $CPROG. Added MAKEFILE.COM
1509 * $CPROG/MAKEFILE.COM: procedure for Solomon was causing a warning but
1510 compilation was not affected. This has been fixed to eliminate warning.
1511 Solomon compiled with case sensitivity.
1512 * Compilation of C code changed due to library.h.
1513 * configure: because of problems with the optimisation the default is
1514 now O1 for OSF1. IRIX6.2 section added. Warning messages have been
1515 surpressed for IRIX5*, HPUX A.09.* and OSF1.
1516
1517 * Program changes:
1518 * AMORE: if the B for an atom is zero or below then it is reset to 20.0. A
1519 message is printed if this is the case.
1520 * BONES2PDB: latest version from KDC on 7/10/96.
1521 * DM: lastest version from KDC on 7/10/96.
1522 acr 1.36 * ECALC: resolution keyword is now acted upon.
1523 * F2MTZ: calls to fatal were incorrect.
1524 * FFT: keyword FILL didn't do anything - fixed. New keyword GRID SAMPLE to
1525 specify the sampling grid as a fraction of the resolution. FFTs in P2 did
1526 not work properly and has been removed. P1 should be used instead of P2.
1527 * FHSCAL: labels DANO and SIGDANO changed to DPH and SIGDPH to be consistant
1528 with SCALEIT.
1529 * IPDISP: spdfils have been changed for MARs. -Ms is now a bigmar with
1530 squashed format. -Mo has been removed but is equivalent to -M. -m small
1531 mar in original format. All these are big endian. -V is the same and
1532 now -v is small mar from VAX i.e. little endian.
1533 * MAMA2CCP4: latest version from KDC on 7/10/96.
1534 * MAPMASK: latest version from KDC on 7/10/96.
1535 * MAPROT: latest version from KDC on 7/10/96.
1536 * MLPHARE: problems with printing MNFs when monitoring reflections fixed.
1537 * MTZ2VARIOUS: typo in defining external function was causing compilation
1538 problems. Now fixed. EXCLUDE FREER will now exclude any freeR subset. Any
1539 FreeR sub-set in the MTZ file can be output as the FreeR set to XPLOR,
1540 SHELX. Dummy columns IDUM?? have been added, these will output as integers
1541 in USER mode. An mmCIF file of the reflection data and associated data
1542 can now be generated. XPLOR output changed to output SIGMA instead of SIGM.
1543 acr 1.36 * MTZDUMP: FORMAT keyword introduced so that the reflection list can be
1544 output in a certain format. Resolution limits are applied to the overall
1545 statistics. Missing reflections are flagged with '?'. Ranges are now calculated
1546 for the partial statistics tables (STATS keyword).
1547 * MTZUTILS: the UNIQUE option data from file 2 was output instead of file 1.
1548 Bug now fixed. Associated columns properly scaled with SCALE option.
1549 * NCSMASK: latest version from KDC on 7/10/96.
1550 * POLYPOSE: Bugs fixed so that default values work if FIX and INCLUDE not
1551 specified.
1552 * POSTREF: the column label 'ABSFAC' and 'SIGABS' have been changed to
1553 'SCALE' and 'SIGSCALE' in order to work with output from SCALA.
1554 * PROCHECK: a write statement in PPLOT was over 132 characters. Changed
1555 the write to avoid this. Only a problem with VMS.
1556 * PROTIN: +PROLSQ & REFMAC the format of the PROTOUT file has changed so
1557 that the files will not be compatible with last version. Change is so that
1558 residue numbers up to 9999 are allowed.
1559 * REFMAC: Output FOM as well. Made P1 default symmetry. Now supports cubic
1560 spacegroups. Defaults have changed since last version please read the
1561 documentation.
1562 * RESTRAIN: updated to version 4.3.5 from Ian Tickle. Isotropic Bs are
1563 written out properly when outputing aniso. Us.
1564 acr 1.36 * ROTAPREP: the way the batches are handled is now more consistant. NBATCH
1565 keyword has been removed, the number of batches is taken from the file
1566 where appropriate. MISBATCH keyword added to specify missing batches.
1567 * SCALEIT: interesting stats. on large isomorphous/anomalous differences
1568 produced for REFINE and ANALYSE modes. Normal probability analysis now
1569 seperates centrics and acentrics. Now outputs Kraut scale instead of
1570 reciprocal.
1571 * SIGMAA: problem with missing FC sorted.
1572 * SOLOMON: CCP4 masks were not being read properly, now fixed. O style
1573 rotation and translation operators do not have to have the header line.
1574 Problems have have been caused when averaging using CCP4 masks, now
1575 resolved.
1576 * TRUNCATE: divide by zero problem fixed. The output now contains H K L
1577 F SD Dano SD F+ SdF+ F- SdF- Imean SD I+ SdI+ I- SdI-. Also, scaling with
1578 the Wilson plot is compulsory.
1579 * XDLMAPMAN and XDLDATAMAN: removed system dependent routines. Altered the
1580 menu and io windows so there are sized flexibly. Also, added command line
1581 qualifier so font for menu can be changed.
1582
1583 * New programs:
1584 * MAKEDICT: will produce TNT or PROTIN dictionary entries from a PDB
1585 acr 1.36 or PROTIN file.
1586 * MATTHEWS_COEF: written by Misha Isupov to calculate the Matthews
1587 coefficient given the cell, symmetry, number of atoms etc..
1588 * RASMOL: RasMol 2.6 (unix and VMS versions) are now distributed with CCP4.
1589 * SCALEPACK2MTZ: Convert SCALEPACK output into an MTZ file. It then must
1590 got through TRUNCATE to convert to Fs.
1591
1592 * Library:
1593 * $CLIBD/(no)chiral_pep*.dic: correction to ARG sidechain.
1594 * $CLIBD/atomsf_neutron.lib: Change atomic number of D to 101 to bring
1595 into line with RBROOK.
1596 * chelp.c: some irregularities fixed.
1597 * chelp.h: machine dependent stuff now in library.h.
1598 * library.c: integer type was incorrectly defined for Big-endian
1599 machines with CONVERT_FROM set.
1600 * library.h: has been created from library.c. This will contain the machine
1601 dependences required for all C programs.
1602 * mtzlib.f: bug in LRREFL fixed; affected BIOMOL programs.
1603 * rwbrook.f: s/r SFREAD moved here from AMORE,MLPHARE,REFMAC,SFALL
1604
1605 * Documentation:
1606 acr 1.36 * RSTATS: document brought in line with prog. FREE keyword added.
1607 * Tutorials: a new set of tutorials have been made in five main areas:
1608 MIR, MR, refinement, density moification and MAD. These procedural scripts
1609 can be found in $CEXAM/tutorial.
1610 * html versions of the documentation for most of the main programs are
1611 in $CCP4/html Point your browser at $CCP4/html/INDEX.html
1612 * x-windows/doc: file names have been changed but essentially the *.txt
1613 files are similar to the old *.doc* files.
1614
1615 * Withdrawal:
1616 * ROTAVATA: will be unsupported in release 3.3. SCALA will become the
1617 recommended program.
1618 * PROLSQ: will be unsupported in release 3.3. REFMAC will become the
1619 recommended program.
1620
|
1621 acr 1.34 Summary of significant changes to CCP4 at version 3.1
1622 ------------------------------------------------------
1623
1624 * Building etc.:
1625 * configure: fftbig, tracer and amore have individual compile
1626 flags for AIX. OSF/1 optimisation reduced to -O1; problem
1627 with FFT SCALE card suggests compiler problem.
1628 * include/environ.def,default.def: refmac files added.
1629 * CPROG:MAKEFILE.COM: typo in linking of refmac corrected.
1630
1631 * Program changes:
1632 * General: A number of programs were found to close files on program
1633 termination. This may cause problems on some machines. Here
1634 is a list of progs. that were changed (not all programs have been
1635 checked): abscale, act, agrovata, almn, contact, coordconv, crossec,
1636 extend, f2mtz, fft, fftbig, gensym, geomcalc, hgen, hklplot, icoefl,
1637 mlphare, mtz2various, mtztona4, npo, pdbset, peakmax, polarrfn, prolsq,
1638 protin, rfcorr, rotaprep, rstats, sortwater, undupl, vectors, volume.
1639 * FFTBIG: compiler/runtime problems caused by undefined LNAN fixed.
1640 * FHSCAL: problem with eof on input corrected. LIST can take a no. > no.
1641 of refls. without crashing. Statistics for old style MTZ the same as
1642 acr 1.34 new.
1643 * FREERFLAG: systematic absences are now not assigned a freeR flag but
1644 are flagged as missing. When using the COMPLETE keyword the freeR flag
1645 information is taken from the MTZ file and not the keyword input.
1646 * HKLVIEW: minv replaced by minv3 because of routine renaming in
1647 modlib.f (see 3.0).
1648 * MAMA2CCP4: problem fixed wrt quotes in call to ccperr.
1649 * MLPHARE: compiler problems caused by undefined CCPNUN fixed.
1650 * MTZ2VARIOUS: keyword NaN replaced by MISS.
1651 * MTZDUMP: missing reflections are printed as "MNF". The VALM keyword
|
1652 acr 1.36 has been removed.
1653 * PROCHECK: now the first atom in *.new is printed only once. CONVAX
1654 has now beenons are printed as "MNF". The VALM keyword
|
1655 acr 1.34 has been removed.
|
1656 acr 1.35 * PROCHECK: now the first atom in *.new is printed only once. CONVAX
1657 has now been added to distribution.
|
1658 acr 1.34 * PROTIN: error in handling of multiple disordered planar groups fixed?
1659 Atoms now must have VDW radii defined. Hence, changes in dictioaries.
1660 * REFMAC: several fixes.
1661 * ROTAPREP: can now convert user-defined format to multi-record MTZ
1662 file (INPU USER).
1663 * SOLOMON: (solomon.c) parameters for rbfro1 were undefined.
1664 * STEREO: keyword CONSTRAIN could not be used, now working.
1665
1666 * Library:
1667 * SYMLIB: maximum no. of symmetry operators increased to 192. Now
1668 consistent with MTZLIB. Error in handling P2 C unique corrected.
1669 * $CLIBD/protin.dic: all atoms have VDW radii defined. Changed OXT and OE
1670 for NFORMYL and NACETYL so they are consistant with OT.
1671 * $CLIBD/protin_jp.dic: extra terminal atoms (OE, OXT) added to terminal
1672 residues similar to protin.dic.
1673 * $CLIBD/protin_vl.dic: extra terminal atoms added to terminal
1674 residues similar to protin.dic.
1675
1676 * Examples:
|
1677 acr 1.35 * *.log-dist: all files except completedata and na4tomtz have been removed
1678 from the $CEXAM/toxd area. Some files have been added to the
1679 $CEXAM/unix/runnable area.
|
1680 acr 1.34 * Solomon.sh: incorrect keyword was changed. Error in reading map files
1681 corrected.
1682 * $CETC/uniqueify: original cell now retained rather than rounded up version.
1683 Problem with some refls. not being assigned a FreeR flag overcome.
1684 -f switch modified to accept <label> argument. -p <fraction> switch added.
1685 * $CETC/UNIQUIFY.COM: added. VMS version of uniqueify
1686
1687 * Documentation:
|
1688 acr 1.35 * hgen: included this time.
1689 * mtzutils: RZONE described correctly now.
1690 * Solomon: MULSOLV keyword incorrectly referenced in the doc as
|
1691 acr 1.34 SLVMUL.
|
1692 acr 1.35 * mtzmnf: clarified that columns not specified in LABIN are output
|
1693 acr 1.34 unchanged.
|
1694 acr 1.35 * unique: improved description of uniqueify script.
|
1695 acr 1.34
|
1696 acr 1.33 Summary of significant changes to CCP4 at version 3.0
|
1697 fx 1.32 ------------------------------------------------------
1698
1699 * Building etc.:
1700 * ccp4/etc/PROCHECK*.COM: hopefully the problem with PRODIR$ is now
1701 sorted.
1702 * XCCPJIFFY: SUNOS_5 added to Imakefile, SUNOS_4 hints in comments.
1703 * Irix6 configuration is provided, your mileage may vary -- it did for me.
1704 Feedback still wanted.
1705
1706 * Program changes:
|
1707 acr 1.33 * AMORE: The HKLM keyword has been reinstated. Default NM=25. Fix: all
1708 0kl reflections of table were 0. Keyword END now accepted. Fix possible
1709 problems with inverse FFT due to dimensioning error. Fix failure to get
1710 FFT prime factors right. Less likely to overflow limits on HKL. SORTFUN
1711 can generate a table -- enables use of Es for TRAFUN. Maximum value for
1712 TRAFUN NMOL <nmol> increased to 9. The ROTATE NSR keyword reinstated.
1713 * CAD: The scale factor is now applied to the correct columns and not to
1714 inappropriate ones like phase.
1715 * DM: correct multi-domain averaging bug. DM 1.6 now current version.
|
1716 fx 1.32 * ECALC: Use LABIN and LABOUT rather than FOBS/ISODIFF -- incompatible
|
1717 acr 1.33 change. Introduced SCALE card to scale F and F2OR.
|
1718 fx 1.32 * F2MTZ: Deal with SHELX free R.
|
1719 acr 1.33 * FFT/FFTBIG: A new keyword has been added FILLIN which substitutes F2 for
1720 F1 if F1 is missing. This only works if the MTZ file has been properly
1721 converted to Missing Number Flags.
1722 * FHSCAL: Resolution card added so that data can be truncated in output
1723 file.
|
1724 fx 1.32 * FREERFLAG: Default semantics of free R column changed, along with its
|
1725 acr 1.33 type: it's picked from a set of integers, allowing full cross-validation.
1726 An existing free R set may be completed when reflections are added (only
1727 if using missing data conventions).
|
1728 fx 1.32 * HKLPLOT: Redimensioning, improved output.
1729 * IPDISP: spdfil.mar_n now image type "bigovf", to indicate overflow
1730 table. ipdisp -m option points to spdfil.mar_n (bigend rather than
1731 littleend image)
1732 * MLPHARE: Phasing power was printed as 0.0 with PRINT AVE. SCALE FP option
1733 removed. Resolution in Angstroms is added to tables but not plotted on
1734 xlog-graphs. SCRIPT keyword will produce either a VMS COM file or unix
1735 script with refined heavy atom parmeters. Ensure Angstrom coordinates are
|
1736 acr 1.33 in PDB format - Orthogonal code 1. Will now produce NaNs for unphased
1737 reflections.
|
1738 fx 1.32 * MTZ2VARIOUS: Remove RESTRAIN input type (never actually necessary
1739 since restrain can specify the input format) now restrain reads MTZ. OUTPUT
1740 USER will now output DP and SIGDP. For USER the ordering of the columns is
|
1741 acr 1.33 taken from the ordering on LABIN not LSPRGI table. If reflection record
1742 has NaN, by default reflection not output. NAN keyword will output them.
1743 * MTZDUMP: Missing data identified through MNFs. File statistics table
1744 now gives single "Mean" and "Mean abs." which is calculated from all
1745 non-missing data in a column. LRES option added to list resolution.
1746 More flexible statistics available via STAT keyword.
|
1747 fx 1.32 * NA4TOMTZ: Fix incorrect call of `qnan'. (Unlikely to have caused problems
1748 before missing data changes.)
1749 * NPO: colours are now consistant with those defined in XCCPJiffy. CHAIN
1750 sub-keyword removed. Input handling improved a little. JOIN RADII HBOND
1751 now works as it should. Msecst has been reinstated. Can now have maps
|
1752 acr 1.33 stacks like 3,5,7 or 5,10,15 etc.. RADII BOND ALL fixed.
|
1753 fx 1.32 * OVERLAPMAP: changed code for EXCLUDE option. Will have non-zero point in
1754 mapout if |grid_point| < 1.0e-06 in map1.
|
1755 acr 1.33 * PDBSET: new keywords added EXCLUDE HEADERS, EXCLUDE HYDROGENS and SEQUENCE
1756 [PDB|SINGLE].
|
1757 fx 1.32 * PHISTATS: output improved + documentation.
1758 * PLTDEV: `-pen' option now works (e.g. for colour PostScript). Colours
1759 are now consistant with those defined in XCCPJiffy.
1760 * PROLSQ: the keyword RTEST has been reconstructed. Now you can only have
1761 RTEST -1|0. This means that you cannot recalculate structure factors i.e.
1762 RTEST +1.
1763 * PROCHECK: Updated to v. 3.3.2 plus fixes.
1764 * PROTIN: Didn't find contacts between the same residue on symmetry related
1765 molecules; error in packed symmtery number caused some contacts not to be
1766 picked up by prolsq; increase some dimensions; error in checking special
|
1767 acr 1.33 inter-chain distances; no longer monitors short hydrogen bonds. Can now
1768 use atom names which represent ions e.g. Fe+2, U+6 etc. Non-protein residue
1769 atoms all assigned as side-chain not as main-chain and side-chain.
1770 * RFCORR: arrays for PARSER redimensioned to avoid problem with TITLE. Polar
1771 angles are output correctly when have exact 2-fold axes.
|
1772 fx 1.32 * ROTAPREP: Format for SCALEPACK options changed from F8.1 to F8.0. Also,
1773 updated man page.
|
1774 acr 1.33 * ROTMAP: the table printed after the OUTPUT ... keyword was incorrect, now
1775 fixed.
|
1776 fx 1.32 * RSPS: Failed to handle SGs with Patterson symmetry groups 143-145.
|
1777 acr 1.33 * RSTATS: OUTPUT ASIN changed to LABOUT ALLIN. PROCESS FOBS should work.
1778 Ranges in F applied to Fobs only. Xloggraph altered and new column added
1779 ln(<Fo>/<Fc>) v resolution.
|
1780 fx 1.32 * SCALEIT: failed for more than 9 derivatives
1781 * SFALL: Reads formfactors automatically if not specified, but still no way
|
1782 acr 1.33 to distinguish Fe Fe+2, Fe+3 except to enter manually. Obsolete keywords
1783 removed.
|
1784 fx 1.32 * SIGMAA: `PARTIAL DAMP' didn't work. HLAC ... HLDC now output correctly.
|
1785 acr 1.33 Map cofficients can now be constructed for missing reflections.
1786 * SORTMTZ: now not only does there need to be an equal number of columns in
1787 each file but the column types must be equal.
1788 * SURFACE: trapped uninitialised variable, important for output.
1789 * TRACER: prog. now works correctly.
|
1790 fx 1.32 * TRUNCATE: MTZ columns were potentially scrambled for data not from
1791 agrovata containing anomalous data.
1792 * ZEROED: initialised some variables to stop IOT trap failure.
|
1793 acr 1.33 * Handling of `missing' data in files added to:
1794 abscale, absurd, agrovata, almn, amore, ecalc, f2mtz, fft, fftbig, fhscal,
1795 freerflag, hklplot, icoefl, mtz2various, mtzdump, mtztona4, mtzutils,
1796 na4tomtz, phistats, polarrfn, postref, rotaprep, reindex, rsearch, rstats,
1797 scala, scaleit, sigmaa, sfall, sortmtz, tffc, truncate, unique, uudupl,
1798 wilson.
|
1799 fx 1.32
1800 * New programs:
1801 * CROSSEC: Interpolate cross sections and compute anomalous scattering
1802 factors (thanks to Don Cromer).
1803 * GEOMCALC: Geomtery calculations on molecule (some overlap with `angles')
1804 * HGEN: Generates hydrogen atoms for a protein coordinate file with standard
1805 geometry.
|
1806 acr 1.33 * MAPROT: Map skewing, interpolating, rotating and averaging program.
1807 * MTZMNF: Attempts to identify missing data in an MTZ file, and replaces
1808 the entry with a Missing Number Flag (e.g. NaN).
1809 * REFMAC: Garib's Maximum Likelihood refinement program. Brand new from York.
|
1810 fx 1.32 * RESTRAIN, TLSANL: `restrain' does constrained anisotropic thermal
1811 parameter refinement using the translation/libration/screw-rotation model.
1812 Its feature list says: refinement with restrained geometry, rigid body,
1813 use of amplitude and phase observations, group anisotropic displacement
1814 parameters, disordered solvent corrections (thanks to Birkbeck group).
1815 `tlsanl' provides TLS analysis. Note restrain's keyword input isn't
1816 in the standard CCP4 form.
|
1817 acr 1.33 * SOLOMON: density modification (phase improvement) by solvent flipping.
|
1818 fx 1.32 * SORTWATER: Replaces `watersort'.
|
1819 acr 1.33 * xdlmapman, xdldataman: have been added thanks to Gerard K.
|
1820 fx 1.32
1821 * Library:
1822 * library.nw removed after too many complaints -- source is now library.c
1823 * lib/data/atomsf.lib has comment section added; some programs which read it
1824 altered as a consequence.
1825 * lib/data/crossec.lib: Data file for `crossec'.
1826 * CCPOPN uses /dev/null and NL: interchangeably
1827 * Fatal errors on diskio files now report the filename in question.
1828 * Packed image routines (for mosflm, ipdisp): New version.
|
1829 acr 1.33 * MODLIB: MINV has been renamed to MINV3. A new routine has been added to
1830 calculate the inverses of nth order matrices MINVN.
|
1831 fx 1.32 * MTZLIB: Facilities for dealing with missing data items. [Null attributes
1832 for relational tuples? -- surely not!] Writing files with this facility
1833 should probably not be done since the programs aren't guaranteed to
1834 swallow the results.
1835 * PARSER: Backslash is now a continuation character like `&' and `-'.
1836 * RESTRAIN dictionaries: chiral_pep4.dic dna.dic nochiral_pep5.dic
1837 chiral_pep5.dic nochiral_pep4.dic
1838 * RWBROOK: Add deuterium to atom list.
1839 * SYMLIB: new routine HKLRANGE.
1840 * symop.lib: correct groups 120, 166, 210, 219, 220, 227, 228. File now
1841 subjected to the overdue check for fulfilling group conditions on the
1842 operators.
1843 * x-windows/XCCPJIFFY/XCCPJiffy: colours changed to be consistant with those
1844 defined in NPO. Also, Xloggraph and xplot84driver pen colours are the same.
|
1845 acr 1.33 * Altered write statements so they do not exceed vms write limit of 132
1846 characters.
|
1847 fx 1.32
1848 * Examples:
|
1849 acr 1.33 * All examples updated, inline with current progs.
1850 * Runnable: crossec.sh, fractional-orthogonal, restrain,
1851 unique-free-R (using new $CETC/uniqueify script)
|
1852 fx 1.32 * Non-runnable: restrain.exam, mlphare-MAD modified
|
1853 acr 1.33 * VMS: tracer.com, surface-volume-calc.com
|
1854 fx 1.32
1855 * Documentation:
1856 * FAQ: the plain text version with searching scripts (ccp4faq) are avialable.
1857 Just type 'ccp4faq'.
|
1858 acr 1.33 * MLPHARE: more information about using MAD data.
|
1859 fx 1.32 * Out-of-date manual-usletter.ps removed -- the current one should print OK
1860 on letter paper anyhow.
|
1861 acr 1.33 * Updates to mtzlib, npo, sfall, sigmaa documentation and the ccp4.1 man
1862 page.
|
1863 fx 1.32
1864 * Withdrawal:
|
1865 acr 1.33 * COMPLETE removed, see unique.doc for replacement procedure.
1866 * FAQ in $CCP4 removed. It will be added to FAQ on the Web.
1867 * ENVELOPE, FLATMAP, RESLICE, PRMAP moved unsupported status.
|
1868 fx 1.32 * LCF2MTZ, EXCHANGE and LCFLIB removed in the hope that everyone's using MTZ
1869 files -- still available from Daresbury if anyone is in need.
1870 * PLUTO removed, should now use NPO.
1871 * WATERSORT was broken, replaced by `sortwater'.
1872
|
1873 fx 1.29 Summary of significant changes to CCP4 at version 2.15
1874 ------------------------------------------------------
1875
1876 * Building etc.:
1877 * configure tries to avoid messing with the `unsupported' directory if it's
1878 not present.
1879 * HPUX: don't set (invalid) amore (non-)optimisation flags. The correct one
1880 reported to be needed, though.
1881 * include/ccp4.setup-dist: Incorrectly (for any system) set _RLD_LIST,
1882 causing chaos with dynamic loading on Irix and similar systems.
1883 * MAKEFILE.COM: can now compile just one designated program with no checks.
|
1884 fx 1.30 * Fix problems building procheck on VMS.
|
1885 fx 1.29
1886 * Program changes:
1887 * CAD: Allow longer LABIN/LABOUT lines. Accept LABIN FILE <i> ALL.
1888 * CONTACT: The output has changed to: Res type, Res ID, Atom name.
|
1889 fx 1.30 * IPDISP: Support MacScience scanner.
|
1890 fx 1.29 * MAPMASK: Symmetry expansion speeded up. New SIGMA option for SCALE
1891 (useful when contouring).
1892 * MTZUTILS: Fix zeroed columns from hklin2 for reflexions not in hklin1 with
1893 UNIQUE option.
1894 * NCSMASK: A crude `sphere mask' can be constructed by making a PDB file
1895 with only a few atoms and specifying a large radius. Output map grid was
1896 always 3A round coordinates -- now 2A+<rad>.
1897 * PEAKMAX: symmetry related peaks at the edge of the map are not output.
1898
1899 * Library:
1900 * QNAN from the diskio routines (almost unused) changed from a function to a
1901 subroutine to avoid lossage with f2c's calling conventions.
1902 * protin.dic: Last block wasn't read. WAT residue changed to contain more
1903 extensive list of waters (oxygen) only. All other atoms (ZN1,CU) have been
1904 removed.
1905 * symop.lib: Errors corrected in SGs 43, 112, 115, 160, 210, 228, 230 (a
1906 subset of errors reported with the X-PLOR version...)
1907
|
1908 fx 1.30 * Examples:
1909 * Remove unnecessary test_brk.brk
1910
|
1911 fx 1.29 * Documentation:
1912 * Several .doc files corresponding to man .1 files were missing. diskio.doc
1913 was out-of-date.
|
1914 fx 1.30 * Various fixes/updates to documents for amore, ccplib, contact,
1915 libsymmetry, lsqkab, ncsmask
1916
1917 * Withdrawl:
1918 The programs scheduled for withdrawl aren't taken out of this realease,
1919 which is mainly to fix bugs.
|
1920 fx 1.29
|
1921 fx 1.26 Summary of significant changes to CCP4 at version 2.14
1922 ------------------------------------------------------
1923
1924 * Building:
1925 * XCCPJIFFY: Fix problems on Convex (but see comments in Imakefile).
1926 * x-windows/README: The note about patches for xdl_view was obsolete.
1927 * HPUX: Get the right version of the date routine under HPUX9. Attempt to
1928 cope with `Convex' variant (gosh).
1929 * Linux (and other) compilation with f2c: now assumes use of the `fort77'
1930 script (untested on Linux so far)
1931
1932 * Program changes:
1933 * AMORE: tidy up keyworded input: some dubious input which previously worked
1934 may now be rejected.
|
1935 fx 1.27 * CAD: errors in keywords are now trapped better.
|
1936 fx 1.26 * DERIV: fixed bug in atom input
1937 * DM: multitudinous ways to enter averaging matrices; skeletonisation
1938 facility; output solvent masks could be ragbled in some SGs
1939 * ECALC: More tables and xloggraph markup.
|
1940 fx 1.27 * FFT: grid sampling for P31(144) is now Nx=Ny=6n Nz=6n, for P21212a(1018)
1941 Ny=4n Nz=2n and for P61(169) Nx=Ny=6n Nz=12n.
|
1942 fx 1.26 * HKLVIEW: reciprocal lattice spacing value in the output area was always
1943 zero during a "measure"; rationalization of maximum resolution handling;
1944 -rawname option.
1945 * MAMA2CCP4: Allow Uppsala compressed format (re. O FAQ Q.731).
1946 * MTZUTILS: Error is produced when two output columns are the same when
1947 using INCL/EXCL. Problem with potentially using random resolution limits
1948 fixed. Now defaults to ONEFILE if HKLIN2 not assigned and also checks for
|
1949 fx 1.27 HKLIN; per old documentation but wasn't implemented previously. UNIQUE
1950 option failed when there were more reflections in hklin2 than in hklin1.
|
1951 fx 1.26 * NPO: RESIDUE EXCL now works as it should. Plus documenation more in
|
1952 fx 1.27 line with program. DCELL now works and map axes labels are always plotted.
1953 Open scratch file in the scratch area.
|
1954 fx 1.26 * PDBSET: new options SYMGEN NCS, SELECT OCCUPANCY; fixed bugs in RENUMBER
|
1955 fx 1.27 input and in reading O datablock; new options BFACTOR MAXIMUM|RANGE,
1956 SELECT BFACTOR, COM, REPLACE ATOM. O data blocks can now have comments and
1957 case insensitive to data block type i.e. R
|
1958 fx 1.26 * PEAKMAX: Output overflow is now fixed.
1959 * POLARRFN: ticks at 0, 90, 180, -90 are now sensible.
1960 * PROCHECK: Version 3.3 (less the NMR stuff). See $CPROG/procheck/README
1961 (no new manual). New script procheck_comp for comparing related
1962 structures (also proplot_comp), both untested.
1963 * PROTIN: Deal with multiplanar groups automatically. Re-dimension to cope
1964 with current default dictionary. VDW contact checks weren't being done
1965 between different chains in the same molecule. More consistency of error
1966 messages so they can be found in the output.
1967 * ROTAPREP: With RAXISDUMP (& WEIS) input only: for MPART>1, IPR would have
1968 a garbage value. For SCALEPACK input: initial records shouldn't be read
1969 as reflexions; strong reflexions were being read wrongly, effectively
1970 divided by 10 because of inconsistent formatting by scalepack.
|
1971 fx 1.27 * RSEARCH: Does dynamic memory allocation.
1972 * RWCONTENTS: Don't write to unconnected unit.
|
1973 fx 1.26 * SCALA: wrong values to be output in the modified SD columns SIGIC,
1974 SIGIPRC, iff the input file contained a SCALE column (ie if the output
|
1975 fx 1.27 file from Scala had been run into the input for further scaling); fix
1976 wrong reflection counts and array overflow with FINAL FULL.
|
1977 fx 1.26 * SFALL: The documentation and some output messages have been amended to
1978 clarify confusion about the setting of nonstandard atom/residue types to
1979 ZZZ/DUM. Some messages are now only output with VERBOSE. PG name could
1980 get corrupted, confusing dm. For P4i2i2 SGs, phase was wrong for centric
1981 reflexions h 0 l with h+l divisible by 3. Now checks for reflexions in an
1982 incompatible AU for the SFSG requested. P3-specific SF and refinement
1983 routines added.
|
1984 fx 1.27 * SIGMAA: map coefficients for PARTIAL and COMBINE changed, new labels --
1985 see doc. Two sets of experimental phases can now be merged (with or
1986 without HL). COMBINE syntax changed. Phase analysis transferred to
1987 PHISTATS.
1988 * UNIQUE: DEAFULT keyword for dummy column contents.
|
1989 fx 1.26 * WATPEAK: bad subroutine call could cause crash. Error fixed in calculation
1990 of symmetry equivalents. Error in output fixed. Dmin default is now 0.1
1991 and output expanded.
1992
1993 * Library:
1994 * KEYPARSE: New module providing a higher-level interface for decoding
1995 keyworded input.
1996 * lib/data/protin.dic: Residue flags corrected per protin change. Fix to
1997 avoid fatal error in protin.
1998 * lib/data/protin_jp.idl: Format error for group DFP causing problems even
1999 when the group not used.
|
2000 fx 1.27 * lib/data/symop.lib: typo in 72th symmetry element of F432 (209).
|
2001 fx 1.26 * MTZLIB,SYMLIB: SYMFR{2,3} no longer reset the start column to 0 and check
2002 for a SYMM keyword there.
2003 * PLOTSUBS: correct coordinate transformations used by PLTDBU, PLTMBU
2004 * PARSER: The IDEC value returned by PARSE(R) was rubbish for integers and
2005 not per doc for reals -- definition for integers rationalised (changed).
2006 * RWBROOK: New routine RCELL to return cell parameters; remove the EJD
2007 feature whereby atom types could be stored in columns 67-80 and clash with
2008 footnotes. In RBROOK atom type ' W' is now Tungsten and not water.
|
2009 fx 1.27 * CCPOPN: Fix the Unix special case for /dev/null with CCP4_OPEN=UNKNOWN.
|
2010 fx 1.26
2011 * New Programs:
2012 * BONES2PDB: Convert BONES output to pdb file.
2013 * MAPMASK: General map and mask manipulation program; can replace `extend',
2014 `envelope', `prmap'.
2015 * NCSMASK: Performs operations on non-crystallographic symmetry masks,
2016 e.g. as a precursor to DM.
|
2017 fx 1.27 * PHISTATS: Phase analysis (the ANALYSE part of the old SIGMAA). NB. It is
2018 probably more informative to do map correlation.
|
2019 fx 1.26 * POLYPOSE: A program for superimposing many multi-domained structures.
2020 Written by R. Diamond.
2021 * PROCHECK scripts, programs: procheck_comp, proplot_comp, mplot, rmsdev
2022 (see above).
2023 * STEREO: To reconstruct 3D coordinates from measurements of stereo diagrams
2024 (from Michael Rossmann).
2025
2026 * Examples:
|
2027 fx 1.27 * For new programs: polypose, stereo
2028 * RF-with-Es, toxd-RF-Es: rotation function with Es
2029 * auto-amore, MR-with-amore: automated running of amore for a simple case
|
2030 fx 1.28 (unrealsitic toxd example removed)
|
2031 fx 1.27 * non-runnable/mapcutting: Prepare P1 map to calculate "model" structure
2032 factors for molecular replacement.
2033 * procheck/procheck_comp: there are VMS examples, although they both can be
2034 run interactively.
2035 * watpeak: Using toxd without the waters as the model. Then generating "new"
|
2036 fx 1.26 waters from an fo-fc map. These new waters can be compared with the
2037 refined ones.
2038
2039 * Documentation:
2040 * (Still insufficient) update of the print{ed,able} manual. It's possible
2041 the description of the distribution in the printed one doesn't quite match
2042 what's here.
2043 * An FAQ is available, for what it's worth.
2044
2045 * Notice of withdrawal:
2046 In the next release PLUTO will be withdrawn in favour of NPO and ROTAVATA
|
2047 fx 1.27 will be withdrawn in favour of SCALA. Also possibly/probably for the chop
2048 as the functionality is elsewhere: extend, reslice, prmap, envelope,
2049 flatmap.
|
2050 fx 1.26
|
2051 fx 1.25 Summary of significant changes to CCP4 at version 2.13
2052 ------------------------------------------------------
2053
2054 * Building:
2055 * Configuration/installation was wrong for dynamic shared library
2056 * Building mosflm-stuff failed if not building a shared library
2057
2058 * Library:
2059 * CCPALC: now zeroes the memory chunk -- affects amore, at least
2060 * protin.dic: New values for protein residues to improve bond angles.
2061 Another co-factor has been added.
2062 * protin_jp.doc: Gives an explanation of how JP dictionary was made. The
2063 default dictionary is based on this.
2064 * SunOS: CCPFYP now sets up abort for common floating point exceptions
2065 * symop.lib: added spacegroup 1003 (P2 with dyad along Z)
2066
2067 * Program changes:
2068
2069 * ALMN: Now reads columns from HKLIN2 correctly.
2070 * AMORE: SIGF is now compulsory. Crashes and garbage output due to
2071 uninitialised data avoided.
2072 fx 1.25 * CONTACT: dimension increased.
2073 * FFT{BIG}: Abcoeffs are now written out correctly.
2074 * NPO: LABEL TEXT wasn't working
2075 * TRACER: input now keyworded and input/output is now to standard
2076 input/output rather than files; avoid crashes on some systems due to
2077 unsaved variables
2078 * WATPEAK: (omitted from 2.12 changes note): SYMMETRY is compulsory because
2079 symmetry related waters are removed.
2080
2081 * Examples:
2082 * Added runnable example for tracer
2083 * waterpeaks now consistent with `watpeak' changes
2084
|
2085 fx 1.23 Summary of significant changes to CCP4 at version 2.12
2086 ------------------------------------------------------
2087
2088 * Building:
2089 * F2C compilation: be conservative about ability to unlink scratch files
2090 (not actually done in 2.11)
2091 * VMS: for DEC fortran remove /noopt in library build and use
2092 /assume=(dummy_aliases) for programs to avoid possible problems with known
2093 illegalities
2094 * A dynamic shared version of the library can be built and installed on
2095 Irix[56] and SunOS5 using the --with-shared-lib option to configure
2096
2097 * Library:
2098 * XDL_VIEW: don't grab inappropriate events with popup
2099
2100 * Program changes:
2101 * ABSURD: allow it ro read antique data
2102 * AGROVATA: fix at 2.11 caused problems with anomalous data
|
2103 fx 1.24 * AMORE: avoid singular matrix from peaksearch on degenerate ridges
|
2104 fx 1.23 * FHSCAL: fix calculation of pseudo cell volume for vecref with multiple
2105 derivatives
2106 * MTZUTILS: didn't find HHL reflections correctly
2107 * NPO: SIG and MAX sub-keywords of CONTRS has been added. Can now contour on
2108 sigma levels or as fraction of the maximum (Atsushi Nakagawa). MAP 3D
2109 option is now reinstated. SYMMETRY input got translation wrong
2110 * PEAKMAX: ensure highest symmetry-related peak not rejected
2111 * PROLSQ: NOUPDATE option expurgated from code and example in doc
2112 * PROTIN: dimensions increased
2113 * REINDEX: avoid /0 etc. problems with null orientation block in input
2114 * ROTAPREP: pick up SIGF column if LABIN not used; abend if no reflexions
2115 passed etc.
2116 * WATPEAK: now has dmin cutoff and will check for symmetry related peaks
2117 to accepted waters.
2118
|
2119 fx 1.20 Summary of significant changes to CCP4 at version 2.11
2120 ------------------------------------------------------
2121
2122 * Building:
2123 * (Unix) binsort didn't get compiled/installed
|
2124 fx 1.23 * IRIX64: 6 is recognised by configure with target `irix' (but we have bad
|
2125 fx 1.20 reports about the 6.0 compiler)
2126 * Irix5.2: avoid X installation misfeature (files installed owned by root)
2127 * F2C compilation: be conservative aboutability to unlink scratch files
2128
2129 * Library:
2130 * XDL_VIEW: bug fixes which probably don't affect ccp4 programs
2131 * lib/data/protin.dic RNA residues have been improved + other changes.
|
2132 fx 1.22 * CCPLIB: correct off-by-one in month value from f2c and AIX IDATE (showing
2133 up in the banner); avoid dates sometimes coming out in US order
|
2134 fx 1.20
2135 * Program changes:
2136 * AGROVATA: numerical problem in rejection in some circumstances; use scala
2137 SIGIC, SIGIPRC columns
2138 * COORDCONV: changes for CSD format at v2.3 were bogus
|
2139 fx 1.21 * CONTACT: translational parts of SYMMTERY were ignored; could fail due to
2140 undefined variables
|
2141 fx 1.20 * HKLVIEW, IPDISP: avoid crash in some circumstances
2142 * MTZ2VARIOUS XPlor output for anomalous data is now correct. Also, DP
2143 sigma cutoff has now been removed.
2144 * NPO the LIMIT keyword works and has been reinstalled.
|
2145 fx 1.21 * OVERLAPMAP: now gives total correlation for main chains and side chains
2146 seperately
|
2147 fx 1.20 * ROTAPREP: check BATCH specification properly and make code easier for
2148 adding new input types
|
2149 fx 1.23 * RSTATS: preserve SIGFC and FREE in output with OUTPUT FOFC
|
2150 fx 1.20 * SCALA: problems with optional columns (manifest with Denzo output, at
2151 least) fixed; Omit "too strong" reflections from initial scaling; New
2152 output columns SIGIC[, SIGIPRC], corrected sd(I), sd(IPR)
2153 * SFALL: potential crashes from unsaved variables
|
2154 fx 1.21 * VECTORS: avoid crashes from coding error
|
2155 fx 1.20
2156 * New programs:
2157 * RFCORR: Analyis of correlations between cross- and self-Rotation functions
2158
2159 * Examples:
2160 * Added runnable examples for: agrovata, rotavata, scala, truncate
|
2161 fx 1.21 * Fixed: tffc_procedure, icoefl
|
2162 fx 1.20
|
2163 fx 1.18 Summary of significant changes to CCP4 at version 2.10
2164 ------------------------------------------------------
2165
2166 * Citation: The appropriate reference for citing usage of the suite is now
2167 Collaborative Computational Project, Number 4. 1994. ``The CCP4 Suite:
2168 Programs for Protein Crystallography''. Acta Cryst. D50, 760--763.
2169
2170 * Building:
2171 * IRIX5.2: [introduced un-noted at 2.8] configure attempts to solve problems
2172 with rewinding scratch files a la 5.1
2173 * rsps compilation ignored the setting of `FC' -- wrong for HPUX, at least
2174 * ipdisp should now build and run under VMS
2175 * `iris3000' configuration removed to avoid confusion with R3000-based Iris
2176 systems -- no evidence it ever worked anyhow
2177 * psaver wouldn't compile e.g. on convex
2178 * AIX: wrong `install' program was used
2179 * VMS: fix makefile.coms for xdl_view, hklview, rsps, creation dates compared
2180 * F2C can be used to compile the suite. This may be of interest to those
2181 who'd otherwise need to buy a compiler. It's adequately fast with gcc.
|
2182 fx 1.19 Use configure flag --with-f2c (unless on linux or freebsd).
|
2183 fx 1.18 * Linux and FreeBSD configurations are available (untested) using f2c
2184 * The `binsort' program has been moved from lib/src to src.
2185 * XDL_VIEW library updated to a newer version that doesn't need patches for
2186 OSF; hklview, ipdisp now use it
2187 * Titan: fixes made but untested
2188
2189 * Library:
2190 * CCPLIB: CCPERR now prints the program name so you can easily see what
2191 failed at the tail of the log file; it should also print error messages on
2192 the unix standard error stream; CCPPNM is a new routine to return the
2193 program name. CCPALC etc. can now cope with 12 arrays, including
2194 LOGICAL*1 (deprecated). CCPOPN messages can now be suppressed using -v as
2195 for QOPEN ones and don't cause write errors with long path names.
2196 * MAPLIB: changed format of mean & RMS density print (Uppsala request); this
2197 might break awk-ward things that look for this information in the old
2198 format-- sorry
2199 * MTZLIB: Change dimensions (and parameterise) to allow 192 symops, not 96.
2200 (3 non-protein groups in symop.lib have this many operators.) LWHSTL is a
2201 new simple interface to LWHIST for writing standard history records. The
2202 mtzlib object size is somewhat smaller. Avoid problems with clashes
2203 between program column labels and file labels when the columns aren't
2204 fx 1.18 actually the same. LOOKUP now initialised as -1 compulsory, 1 soft
2205 compulsory (for agrovata/rotavata etc.) and 0 optional. Other programs
2206 have also been affected.
2207 * pack_c.c: add AIX, HPUX calling conventions
2208 * PARSER: various long-standing lossage in PARSE and PARSER corrected,
2209 especially handling of comments and continuations; now works as documented
2210 in ccp4.1 and the manual, I think. Documentation somewhat improved.
2211 * RWATOM: deleted -- Dimaond format no longer supported by any programs
2212 * SYMLIB: Change dimensions a la MTZLIB; EPSLN now general; some changes to
2213 point group name handling in PGNLAU for consistency with Int Tab.; P61/P65
2214 now NZ=12n.
2215 * symop.lib: typo in SG166
2216 * MAPLIB: Change dimensions a la MTZLIB
2217 * scatcoef.lib obsoleted by changes to vecref
2218 * PLOTSUBS: add routines moved out of polarrfn
2219 * lib/data/hist.lib: added for dm
2220 * lib/data/protin.dic: replaced by John Priestle's, based on Engh/Huber
2221 parameters with York cofactors added.
|
2222 fx 1.19 * lib/data/protin_vl.idl: alternative protin dictionary from Victor Lamzin
2223 (see lib/data/protin_vl.doc)
|
2224 fx 1.18 * BINSORT: programs that do sorting now should always abort (ungracefully)
2225 on disc full errors etc. rather than reporting zero records returned from
2226 the sort and continuing.
2227
2228 * Program changes:
2229 * AGROVATA: partials weren't handled correctly for non-mosflm data; avoid
2230 the need for SCALE with 1 batch; fix array bound errors with all batch
2231 nos. 1
2232 * AMORE: TABFUN accepts NOSHIFT or NOTRAN equivalently; fix failure of
2233 TABLING on some systems due to not closing scratch files; error in
2234 calculation of RF standard deviations; errors in treatment of Miller
2235 indices (which could cause spurious failures) corrected but means that
2236 previously-generated HKLPCK and TABLE files need to be regenerated; TRAFUN
2237 failed in polar space group
2238 * AREAIMOL: potential problems due to uninitialised variables; check for
2239 atomic number written at the end of a PDB line for cases of nonstandard
2240 atom naming, like sfall.
2241 * BAVERAGE: changes to output
2242 * CAD: RESOLUTION OVERALL wasn't obeyed
2243 * EXTEND: proper action if symmetry mangled: if SG number <= 1, set to P1,
2244 else bomb with message; make check against asymmetric unit volume a
2245 fx 1.18 warning, so that it can work in projection
2246 * FFT: Grid in P61/P65 must now be NZ=12n.
2247 * FHSCAL: can scale up to 20 datasets; BIAS now defaults to 0 (assuming the
2248 worst of the data processing program).
2249 * FREERFLAG, MLPHARE, REINDEX, SFALL, SIGMAA: add history to HKLOUT
2250 * HKLVIEW: draws labelled axes
2251 * IPDISP: correct calculated resolution of outer circle. Async I/O removed
2252 to work on OpenVMS. Dialogue box no longer locks screen.
2253 * MAPSIG: keyworded; could loop on default input due to uninitialised
2254 variable
2255 * MLPHARE: Parameters reset properly HLA .. HLD and FHn, FHAn are now
2256 correct on output. LABOUT ALLIN works + program checks to see if input
2257 column labels are the same as program labels.
2258 * MTZ2VARIOUS: TNT output option and EXCLUDE FREER option; USER output
2259 option; SHELX output flagged for free R if appropriate
2260 * MTZDUMP: include zero values of type H, P or A in the resolution
2261 statistics
2262 * NPO: LABEL FIX atom_name and LABEL atom_name now work properly. LABEL
2263 atom_name was not accually possible before. Also input cards echoed in
2264 output.
2265 * OVERLAPMAP: PATTERSON option (a la GROPAT)
2266 fx 1.18 * PDBSET: REORTHOGONALIZE and REPLACE RESIDUE options
2267 * PEAKMAX: symmetry-related peaks not output
2268 * PLTDEV: fixes to scaling for PostScript output
2269 * PRMAP: end-of-file on input now just prints map header
2270 * PROCHECK: version 3.0.1 as released by Roman Laskowski, but with some
2271 programming errors fixed and using CCP4 file opening routines. Includes
2272 colour plots etc. New manual in $CDOC/procheck.doc and
2273 $CCP4/manual/procheck/manual.ps. Note the accompanying licence in
2274 $CPROG/procheck/confid.doc
2275 * PROTIN: default dictionary improved (see above)
2276 * ROTAPREP: reading XDS files and F+, F-, sigmas are now root(2)*SIGIMEAN.
2277 * ROTAVATA: didn't accept MAXWIDTH keyword to pass to agrovata; fail
2278 gracefully when zero reflexions accepted in a batch
2279 * ROTMAT: wouldn't run without complaining about missing CRYSTAL; slight
2280 additions to output
2281 * RWCONTENTS: count of hydrogens was wrong
2282 * SCALA: Made phi range errors warnings up to maximum of 50 errors; SKIP
2283 option; OUTPUT OMIT PARTIALS option: Don't keep partials if not being used
2284 for scaling (should speed things up)
|
2285 fx 1.19 * SCALEIT: now defaults to NOWT option (ignore SDs of data); new keyword
2286 WEIGHT to use SDs.
|
2287 fx 1.18 * SFALL: Improve some error messages; SFSG now defaults to an appropriate
2288 value (highest symmetry consistent with the data) so you don't have to
2289 look one up. Grid in P61/P65 now NZ=12n. LABOUT ALLIN works + program
2290 checks if input column labels are the same as program labels. Using
2291 FPART PHIPART was broken.
2292 * SIGMAA: new option to set resolution limits for phase combination
2293 ("COMBINE LOW|RESOLUTION")
2294 * TFFC: allow much longer buffer for entering input label assignments which
2295 may be needed in some cases
2296 * VECREF: new keywords RCUT, DAMP; use atomsf.lib scattering factors rather
2297 than scatcoef.lib; improved treatment of large Bs; sites with low
2298 occupancy or silly B factors not output; allow negative occupancies; THRE
2299 & BLIM options; dynamic memory allocation.
2300 * WILSON: END keyword; coding error caused failure sometimes
2301
2302 * New programs:
2303 * DM: all-singing, all-dancing density modification: solvent flattening in
2304 one program, histogram mapping, Sayre's equation, molecular replacement...
2305 See also the document doc/dm_ncs_averaging.doc
2306 * MAMA2CCP4: convert Uppsala-format masks from MAMA to CCP4 format (`mapman'
2307 isn't currently correct on this)
2308 fx 1.18 * RESLICE: A simple-minded resectioning program; interchanges axes in core
2309 ("unsupported")
2310 * STNET: Generate stereographic net plot for use with polarrfn
2311 ("unsupported")
2312
2313 * General:
2314 * History records written to HKLOUT now mostly have date and time included
2315 to give a better chance of figuring out sequences if necessary.
2316 * Keyworded input may give less unpleasant surprises now due to fixing of
2317 `parser'
2318 * Vestiges of Diamond format coordinate files removed
2319
2320 * Examples:
2321 * Original toxd dataset had wrong column type for ANAU20
2322 * examples/vms is now much fuller
2323 * Updated or added examples in examples/unix/runnable: mir_steps, vecref.sh,
2324 scaleit.sh, patterson (replaces fft.sh), dm.sh, 3fofcmap, f2mtz.sh &
2325 mtz2various.sh (using free R and X-PLOR type), rsps.sh, fhscal.sh,
2326 polarrfn.sh, scaleit.sh, mtzutils.sh, npo.sh
2327
2328 * Manual:
2329 fx 1.18 * Minor changes to the text -- no new printed version currently.
2330 * To format the LaTeX for US letter paper (rather than A4) uncomment
2331 `\letterpapertrue' at the top of manual.tex and run `dvips' appropriately.
2332 The result is now available as manual-usletter.ps.
2333
2334 Summary of significant changes to CCP4 at version 2.9
2335 -----------------------------------------------------
2336
2337 * VMS: reading MTZ files basically didn't work from v2.7 -- records were
2338 essentially all zeroed under most circumstances
2339
2340 Summary of significant changes to CCP4 at version 2.8
2341 -----------------------------------------------------
2342
2343 * Building:
2344 * PSAVER wouldn't build under DEC Fortran (broken at 2.7, sigh)
2345 * VMSDISKIO compiled with some fortran versions, despite containing junk,
2346 but not with others
2347
2348 * Library:
2349 * PARSER: avoid problems with @-included files which, e.g. caused `unknown
2350 fx 1.18 keyword' problems with @-files of solutions read back into amore
2351 * SYMOP.LIB: 2 typpos: `_' for `-'
2352
2353 * Program changes:
2354 * MLPHARE: Bug for MAD data: it assumed it could estimate the centric phase
2355 from the the first FH, which doesn't work if your first FH = 0.0.
2356 * SFALL: UnSAVEd variables could cause failure sometimes
2357
2358 Summary of significant changes to Csignificant changes to CCP4 at version 2.7
|
2359 fx 1.14 -----------------------------------------------------
2360
2361 * Building:
2362 * HPUX: Enable some floating point traps in OS v9 and remove abort on all
2363 other signals
2364 * The `ranlib' step was omitted after the mosflm-stuff target in the
2365 library; affects BSD-like unixes
2366 * VMS: The MAKEFILE.COMs would only work with DEC Fortran (OpenVMS) (?)
2367 through using a .F extension
2368
2369 * Library:
2370 * IRIX 5.1: enable rewinding of scratch files (at the expense of them not
2371 being deleted if the program crashes); there may be other problems with
2372 irix5.1
2373 * IPDISP: changes for building in VMS (yet untested)
|
2374 fx 1.17 * MAPLIB: MSYCPY mangled the symmetry information if maps were transported
2375 between machines with different byte orders; affects programs extend,
2376 overlapmap, mapreplace, zeroed
|
2377 fx 1.14 * MTZLIB: speed up reading and writing MTZ files somewhat by avoiding a
2378 subroutine call for each datum
2379 * VMSDISKIO: efficiency improvements and QINQ now works (but never used?)
|
2380 fx 1.15 * XDL_VIEW: typo prevented compilation; Makefile altered; (untested) VMS
2381 MAKEFILE.COM
|
2382 fx 1.14
2383 * Program changes:
2384 * AGROVATA: removed VAXtran; BINS RECIPROCAL option allows binning by equal
2385 volumes in reciprocal space
2386 * BAVERAGE: code polished
|
2387 fx 1.16 * COORDCONV: fix possible uninitialised variable; maybe speed up reading of
2388 X-PLOR format
|
2389 fx 1.14 * FFT{BIG}: coding error caused core dumps in some cases
2390 * MLPHARE: increase maximum refinement cycles
2391 * MTZUTILS: resolution restriction didn't always work with two files
2392 * PEAKMAX: The incorrect peak height (NEXT peak in the sorted list rather
2393 than current) was being written to the output Brookhaven file in the
2394 "occupancy" column.
2395 * PROLSQ: VDW contacts not used properly; fixes to allow variable
2396 non-crystallographic symmetry
2397 * PROTIN: fixes to allow variable non-crystallographic symmetry; increase
2398 maximum number of atoms
2399 * ROTAVATA: BINS RECIPROCAL allowed in line with agrovata
2400 * ROTMAT: insist on CRYSTAL input
2401 * SCALA: bugs affecting INTENSITIES PARTIALS option
2402 * SFALL: source code re-vamped; error with ALLIN and >29 columns; problem
2403 with error estimate could cause failure; removed SAVEs to give
2404 optimisation a better chance.
2405 * SIGMMA: phase analysis instrumented for xloggraph
2406 * VECTORS: allow atom lines to have extra fields on end
2407 * WATPEAK: two new totals; dimensions increased
2408
2409 * Documentation changes:
2410 fx 1.14 * FFT: correct some SG-dependent info
2411 * FHSCAL, VECREF: minor changes
2412 * ROTMAT: more explanation/clarification
2413
2414
2415 Summary of significant changes to CCP4 at version 2.6
2416 -----------------------------------------------------
2417 * Building:
2418 * SYMLIB: non-standard fortran
2419 * OSF/1: unaligned access wasn't fixed
2420
2421
|
2422 fx 1.13 Summary of significant changes to CCP4 at version 2.5
2423 -----------------------------------------------------
2424
2425 * Building:
2426 * Typpos caused failure on: ESV (/Titan?), VMS
2427 * OSF/1: `make' infelicity caused failure; OSF check missing from chelp
2428 (mosflm bits only); OSF `fsplit' failed on rwbrook.f, symlib.f; mtzlib
|
2429 fx 1.14 caused unaligned access errors on OSF/1 (generally wrong for 8-byte C
|
2430 fx 1.13 longs)
2431 The xdl_view-based code won't work asis (due to 64-bit pointers).
2432 `x-windows/osf-patches' supplies patches specific to OSF/1 pending a new
2433 version of xdl_view.
2434 * AIX: amore optimisation flag wrong
2435 * VMS MAKEFILE.COMs now try to reset working directory sensibly
2436 * SCALA directory needed re-naming for make to work
2437 * MSTAMP omitted from makefile
2438 * RSPS sometimes printed symmetry operators wrong
2439 * ccp4.setup-dist had a typo in the XUSERFILESEARCHPATH definition
2440
2441 * Library:
2442 * Dynamic memory allocation was wrong for integer arrays -- they only got
2443 half as much as they should have done. Might have affected amore results.
2444 * CCPLIB: add CCPNUN for finding unconnected i/o unit.
|
2445 fx 1.14 * QSEEK errors now hint that the file may be corrupt.
|
2446 fx 1.13 * PARSER: avoid echoing lines when reading `@'-file e.g. symmetry headers
2447 from agrovata
2448 * SYMLIB: SYMTRN was wrong for operators n/4
2449
2450 * Program changes:
2451 * AMORE: improve error messages
2452 * HKLVIEW: can display columns other than of type F or J (eg W)
2453 * IPDISP: minor changes and new detector types
|
2454 fx 1.14 * MLPHARE: minor corrections - aniso eigen vectors not printed
|
2455 fx 1.13 * PLTDEV: fix picture range selection
2456 * SCALA: cope properly (?) with absent orientation blocks; if scaling with
2457 fullys only, skip reflections with le. 1 full (this speeds things up a lot
2458 in many cases); doc change
2459 * SFALL: didn't cope with an MTZ file with RESO 0
2460 * XCCPJIFFY: changes for OSF/1 had been omitted
2461
2462
|
2463 fx 1.11 Summary of significant changes to CCP4 at version 2.4
2464 -----------------------------------------------------
2465
2466 * Building:
2467 * library.c wouldn't compile with Sun bundled compiler and probably other
2468 K&R ones
2469 * amore optimisation flag was invalid on Sun with SunPro compiler (at least)
2470 * rsps compilation flags changed for Irix to try to avoid v. long
2471 compilation and reported compiler crashes
2472
2473 * Library:
2474 * SYMLIB: PG 321 was written out with the `PG' missing
2475 * PARSER: bug with lines exactly 133 characters long
2476
2477 * Program changes:
2478 * AGROVATA: fix in absence of MPART column
2479 * AMORE: rotfun could output garbage; dimension was set incorrectly for
2480 sorting step
2481 * BAVERAGE: error in xloggraph output
2482 * DISTANG: change error report
|
2483 fx 1.12 * ECALC: coding error with PG name
2484 * FFT: wasn't removing scratch file (at least in VMS)
|
2485 fx 1.11 * GENSYM: can now generate more than one cell
2486 * MLPHARE: can now use 20 derivatives
2487 * MTZ2VARIOUS: read Is ready for SHELX
2488 * NPO: bugs in GRID command
2489 * PDBSET: add ELEMENT option; typo could cause bad error message
|
2490 fx 1.12 * POLARRFN: small error in calculation of mean & rms
|
2491 fx 1.11 * RSPS: attempt to remove illegal code had broken the command loop --
2492 current version may not compile (correctly)
2493 * ROTAPREP: fix batch number for XDSUNIQUE, TEXHKL, MUI, MUF; generalise (?)
2494 DENZO
2495 * RSTATS: error for PROCESS FOBC (width multiplied by scale factor for every
2496 reflection)
2497 * SCALA: flow.h and refflg.h were missing; make XDET, YDET, ROT columns
2498 optional if not used
2499 * SCALEIT: can now use 20 derivatives
|
2500 fx 1.12 * TFFC: coding error with PG name
|
2501 fx 1.11
2502
|
2503 fx 1.10 Summary of significant changes to CCP4 at version 2.3
2504 -----------------------------------------------------
2505
2506 * Administrivia: CCP4 is now funded by the Biotechnology and Biological
2507 Sciences Research Council following the demise of SERC. Note also the new
2508 FAX number for CCP4 if you need it.
2509
2510 * Change policy to avoid the distinction between major and minor released
2511 versions: too much work and scope for mistakes.
2512
2513 * Most Fortran files now .f rather than .for as required ages ago by the
2514 Working Group: more convenient on un*x and no problem on VMS.
2515
2516 * VMS library: C code replaced by (faster) VMS-specific Fortran
2517 (vmsdiskio.for), avoiding an apparently insurmountable RTL library bug. The
2518 script MOSFLMBITS.COM an be used to build the extra library modules for
2519 MOSFLM if required.
2520
2521 * Free R factor facilities: programs affected (only additions): freerflag,
2522 sfall, fft, mtz2various, f2mtz, rstats. Note the opposite convention to
2523 X-PLOR -- free R flag is a weight (but not yet used as such). The
2524 fx 1.10 conventional way to arrange calculation of the free R from an mtz file is by
2525 using `LABIN FREE=FreeR_flag'. See individual program documentation and
2526 some altered examples.
2527
2528 * Manual and examples: various fairly minor updates.
2529
2530 * Library:
2531 * changes on termination: try to give helpful system error message and not a
2532 misleading one, fix problems with EXIT on AIX, HP-UX and ISATTY on AIX;
2533 * Some scratch files weren't being deleted under Irix. They should now
2534 vanish, possibly unless the program crashes.
2535 * [ccplib] CCPALC, CCPALE, CCPE2I: facility for dynamic memory allocation
2536 (mainly for amore so far); correct handling of `-d' command-line flag.
2537 * [diskio] MSYWRT: added; properly-typed variants of QREAD/QWRITE: QREADR
2538 etc.;
2539 * [modlib] RANMAR, RMARIN: random number routines added
2540 * `magic number' code for absent data flags was completely bogus, fortunately
2541 not used;
2542 * add CCPMVR, CCPZR, CCPCPI;
2543 * SYMLIB: avoid possibly echoing symop file due to undefined variable;
2544 changes in step with symop.lib PG changes; remove 80-character limit on
2545 fx 1.10 SYMMETRY input.
2546 * PLOT84LIB: tidying up and removal of undefined variables
2547 * Fix problems with read/write diskio files on SunOS, ESV, Titan, at least.
2548
2549 * lib/data/symop.lib now has all standard SGs (and some non-standard) and
2550 correct PG names; symop_all.lib removed.
2551 * lib/data/protin.dic: format error in the planar restraints of the NACETYL
2552 group
2553 * lib/data/VLdict.dic was bogus -- removed. The default protin dictionary
2554 is what this was supposed to be.
2555
2556 * Installation:
2557 * Titan may now work;
2558 * VMS .com files changed, especially for `make'-like facility in
2559 CPROG:MAKEFILE.COM to avoid re-building up-to-date programs; now don't
2560 need a C compiler for the basic library (as above);
2561
2562 * New programs:
2563 * REBATCH: alter batch numbers in an unmerged MTZ file (saves running Mosflm
2564 again); beware -- not well tested.
2565 * FREERFLAG: tags each reflection in an MTZ file with a flag;
2566 fx 1.10 * MSTAMP: add machine stamp to MTZ or map files lacking it (unsupported);
2567 * PSAVER: partial symmetry averaging;
2568 * SCALA: scale together multiple observations of reflections (rotavata
2569 replacement, previously aggregated);
2570 * SYMFIT: fit best molecular transformations to sets of coordinates related
2571 by non-crystallographic symmetry (unsupported).
2572 * X-WINDOWS THINGS: the XLOGGRAPH, XPLOT84DRIVER, IPDISP and HKLVIEW
2573 programs are now considered part of CCP4 (previously aggregated). The
2574 sources live in $CCP4/x-windows. They aren't built and installed with the
2575 rest of the programs. Modify the makefiles in the individual directories.
2576
2577 * Withdrawn:
2578 * HEAVY: use mlphare;
2579 * POLSIG: unnecessary with current polarrfn.
2580
2581 * Program changes:
2582 * ACT: wouldn't run in many cases;
2583 * AMORE: dynamic memory allocation -- can change dimensions without
2584 recompilation (but doesn't necessarily reduce the virtual memory needed);
2585 small fixes; some Spanish translation!
2586 * AGROVATA: Re-dimensioning. FSAFE option now works. Added WIDTH WILSON &
2587 fx 1.10 WIDTH SQUARE options for alternative binning on intensities. Change
2588 binning of partial bias correction analysis to allow bias of +-20% rather
2589 than +-10%. Significant changes to allow addition of partials spanning
2590 more than 2 images, and to make use of the new column MPART containing the
2591 partiality indicator output by MOSFLM. These changes are essential to
2592 deal with data from MOSFLM version 5.20 or later versions. New keyword
2593 MAXWIDTH specifies maximum allowed width (in images) for partials.
2594 * BAVERAGE: correct format error
2595 * CAD: default resolution to agree with documentation; got lattice type wrong
2596 * COORDCONV: changes for SHELX and Cambridge database input; code tidied
2597 * ENVELOPE, FLATMAP: Avoid use of logical*1 true/false in mode0 map -- can't
2598 transport results between compilers.
2599 * EXTEND: remove check on input map starting at grid point 0,0,0, also fixed
2600 minor bug (which caused some unnecessary work in a few cases). Assumed
2601 (incorrectly) that all asymmetric units were mapped from point (0,0,0).
2602 * F2MTZ: `X' column type for X-PLOR free R fudge; correct format error in
2603 example.
2604 * FHSCAL: END keyword, runnable example.
2605 * FFT{BIG}: defaults for Patterson SG were broken. SG47 was not actually
2606 wrong if not defaulted, contrary to previous alarm. fftbig now does
2607 dynamic memory allocation. HKLMAX option for anisotropic resolution
2608 fx 1.10 (strongly discouraged for normal use). Allow explicit symmetry operators
2609 without bombing. Allow sensible input of multiple scales [Bfactors] from
2610 the same line. Logic error for phase of reflexions with |Fph(calc)|=0 in
2611 double difference maps.
2612 * GENSYM: now writes out CRYST1 & SCALE lines to PDB file; new READ option;
2613 ATOM lines can have extra fields.
2614 * LSQKAB: dimensions increased
2615 * MLPHARE: output tidied; redimensioning; all reflections written out even
2616 if not phased; correct labels for 5th, 6th derivatives
2617 * MTZ2VARIOUS: Free R flag added and o/p compatible with X-PLOR. For any
2618 phase columns present must negate the phase when generating the Friedel
2619 pair. This applies to solvent correction term and PHIB term. Option to
2620 read columns DP, SIGDP, ISYM for anomalous differences, to write out hkl &
2621 -h-k-l if Danom present. Avoid mangling indices sometimes. Didn't reject
2622 reflections with SIG=0.0. EXCLUDE, FPMAX, FPHMAX, FSQUARED, SCALE
2623 options. RESTRAIN o/p type.
2624 * MTZTONA4/NA4TOMTZ: run-length encoding option; NaNs in the file handled
2625 properly (for use with absent data when implemented elsewhere).
2626 * MTZUTILS: SCALE option.
2627 * NPO: avoid calling GETENV (bogus in VMS); fix for different contour
2628 colours at some level
2629 fx 1.10 * OVERLAPMAP: ADD option
2630 * PDBSET: UTOB option
2631 * PLTDEV: not outputs conforming PostScript; default scaling still broken.
2632 * POLARRFN: correct logical name COEFFS; NOPRINT option
2633 * PROCHECK: coding corrections. Un-mangled procheck.doc. Note that there
2634 is a newer version available from
2635 ftp@bsmcha1.biochem.ucl.ac.uk:pub/procheck for which we don't have
2636 distribution permission and which isn't for commercial use. v3.0.1 has
2637 coding problems with undefined/unsaved variables for which you can get a
2638 patch from us if these cause problems.
2639 * PROTIN: check VDW contacts in first chain when only one chain present.;
2640 re-dimensioned; default NCODE = 1 (only matters if you input CELL here);
2641 check array bounds and report all errors in input at the end.
2642 * ROTAPREP: reorganise code to make additions easier; update documentation,
2643 especially lies about formats; fix bad batch numbers with DENZO input;
2644 BATCH compulsory; SCALEPACK input only wrote the first I which broke
2645 rotavata with INTENSITIES PROFILE
2646 * ROTAVATA: avoid array bound errors and undefined variables.
2647 * ROTMAT: corrections, particularly for Merlot NCODE.
2648 * RSPS: updated version from Stefan Knight;
2649 * RSTATS: partial re-write and add free R.; END keyword; avoid infinite loop
2650 fx 1.10 due to numerical problems
2651 * SFALL: disallow both RMSSHIFT and STEPSIZE; free R factor; use NOSCAL if
2652 map input; other alterations, especially for ARP use.
2653 * TFFC: SPACEGROUP/SYMMETRY now optional.
2654 * WATPEAK: would only read first chain; write coordinates of each peak to LP
2655 output
2656
2657
2658
2659 Summary of significant changes to CCP4 at version 2.2.4
2660 -------------------------------------------------------
2661
2662 * abscale: over-long format
2663 * act: wouldn't run in many cases
2664 * agrovata: avoid integer overflow
2665 * cad: default resolution agrees with doc
2666 * gensym: wasn't built by unix Makefiles
2667 * mlphare: long-standing error in figure of merit table
2668 * prolsq: wasn't listing bad distances
2669 * rotaprep: wrong for TEXHKL; initialise some variables (e.g. gave bad batch
2670 with denzo)
2671 fx 1.10 * rotavata: assumed static allocation
2672 * rsps: bad format writing score table
2673 * sfall: problem if SMIN = 0.0
2674 * watpeak: would only read first chain
2675 * examples/toxd/solflat-cyc: add NOSCALE in sfall
2676 * lib/data/protin.dic: format error
2677 * mtzlib: error in Groningen changes in LRREFF possibly causing
2678 reference of unset variable; LWBTIT incorrect: affects rotaprep
2679 output, in particular
2680 * build on AXP VMS: problems with com files, C code; allow for vax number
2681 format
2682 * vms library: prints process time at end, not session
2683
2684 Summary of significant changes to CCP4 at version 2.2.3
2685 -------------------------------------------------------
2686
2687 * scaleit: problems with xloggraph o/p
2688 * almn: bad rms density calculation
2689 * deriv: didn't open hklin
2690 * mtzvarious: correct X-plor o/p
2691 * library:
2692 fx 1.10 * problems with rewinding some scratch files on Convex, ESV; setting logical
2693 NATIVEMTZ ignores file machine stamp in reported VMS case where files had
2694 bad stamp
2695 * problems with CCP4_OPEN hadn't been properly corretced at 2.1.1, sigh
2696 * ESV: avoid configure lossage if /usr/ucb isn't on path (shouldn't it be?)
2697 * examples: correct peakmax o/p in a couple of cases
2698 * proclean: uninitialised variables corrected (probably doesn't matter)
2699 * exchange: wouldn't write the LCF file (the only place it's allowed)
2700 * mosflm bits (image packing) wouldn;t build on osf/1
2701
2702 Summary of significant changes to CCP4 at version 2.2.2
2703 -------------------------------------------------------
2704
2705 * binsort building still failed (some unix only)
2706
2707 Summary of significant changes to CCP4 at version 2.2.1
2708 -------------------------------------------------------
2709
2710 * configuration/building: error building rsps (unix) and procheck (VMS) and
2711 binsort (some unixes). Other changes for Concentrix only.
2712 * polarrfn: plotting error
2713 fx 1.10 * prolsq: check for BATOM set but not XYZB in sfall
2714 * protin: long standing error affecting intra-chain special distances
2715 * Library errors causing general problems:
2716 * setting CCP4_OPEN other than to UNKNOWN was treated wrongly in some cases
2717 * maplib: serious array bound error
2718 * parser: failure to read E-format real numbers
2719 * lib/data/symop_all.lib: corrected
2720 * examples/unix/runnable/waterpeaks: previously omitted
2721
2722 [Note that polsig is actually obsoleted by changes to polarrfn.]
|
2723 ccp4 1.1
|
2724 fx 1.3 Summary of significant changes to CCP4 at version 2.2
2725 -----------------------------------------------------
|
2726 ccp4 1.1
|
2727 fx 1.4 * Binary file transparency: the low-level i/o routines can now read MTZ and
2728 map files written on architectures with different number formats *providing
2729 they are written with this version of the library*. There is some overhead
2730 in this, but no significant overhead reading files written on the same
2731 architecture.
|
2732 fx 1.2
|
2733 fx 1.4 Note that not all the possible combinations have been tested...
|
2734 fx 1.2
|
2735 fx 1.8 * Categorisation of programs: There is a new `unsupported' category of
2736 programs. (This does not imply that we guarantee support for the others.)
2737 They are supplied asis and we will not necessarily fix them (but still
2738 welcome bug reports or your fixes). Many obsolete programs have been thrown
2739 out completely. You can install only the major programs and not the
2740 unsupported category if you want. There is a new directory: `unsupported'.
|
2741 fx 1.3
|
2742 fx 1.4 * Documentation
2743 * There is a much-expanded, but still incomplete new manual. This includes
2744 material formerly in the `overview' man `page'.
2745 * new directory man/man3 for library man pages (incomplete)
2746 * There is now a document for every program (we hope) and many have been
2747 much revised and improved. Complete formatted copies are supplied, along
2748 with man `whatis' files and the .doc files can be used with the unix man
2749 system. Most of the documents have been examined and revised.
|
2750 fx 1.2
|
2751 fx 1.4 * Examples: the examples/unix/runnable directory has scripts which will run
2752 with the small dataset from examples/toxd (which also contains working
2753 scripts). The `ctest' directory has been removed.
|
2754 fx 1.8
2755 * VMS library support: the VMS assembler routines have been dropped -- we now
2756 only provide the C version of the low-level library routines since we can't
2757 maintain the assembly code.
2758
2759 *You need a C compiler for the VMS compilation now.* See the manual for how
2760 to get the free GCC compiler if necessary (although this hasn't been tried
2761 for building the suite).
2762
2763 The C routines are slower than the old assembler ones -- sorry. If this
2764 proves to be a particular problem, let us know.
|
2765 fx 1.3
2766 * Changes/fixes to configure and makefiles and VMS installation; the latter is
|
2767 fx 1.4 now simpler and cleaner but is not guaranteed in OpenVMS yet -- please let
2768 us know.
|
2769 fx 1.2
2770 * Library bug fixes
2771 * mtzlib: IPRINT=4 didn't print symmetry any more; user label input and
2772 output variables reset in lropen and lwopen
|
2773 fx 1.3 * some timing routines were wrong
|
2774 fx 1.4 * the setting of CCP4_OPEN is now obeyed for MTZ and map files
|
2775 fx 1.7 * BINSORT alignment problem on some architectures
|
2776 fx 1.9 * possible inability to redefine logical names in VMS
|
2777 fx 1.2
2778 * General library updates
2779 * MODLIB: routines removed: match, ma21ad, mc10ad
|
2780 fx 1.5 * MTZLIB: more batches allowed; interpret absence flags from the Groningen
2781 BIOMOL system (just set to zero at present)
|
2782 fx 1.2 * SYMLIB: routines removed: turnip, turn3, decsym, syminv, iminv,
2783 symat; added: patsgp; changes to symop.lib; more batches allowed; new
2784 library data file symop_all.lib has all Int. Tab. A SGs
2785 * FFTLIB: added routines factrz, fndsmp, setlim, setgrd
|
2786 fx 1.4 * GRAFLIB: no longer included by default. routines now in PLOTSUBS removed
|
2787 fx 1.2 * PLOTSUBS: replaced with routines removed from graflib
2788 * removed modules: graphics, hlplib, mdflib, optfftlib, plot9x, lib_kraulis,
2789 frodo_maplib, mthlib, hdrlib
2790 * LCFLIB now won't *write* LCF files
|
2791 fx 1.3 * `ccperr' now tries to report the last system error and times in VMS
|
2792 fx 1.4 * PARSER: new routines RDRESL, GTTREA, GTTINT; the (mis)feature of allowing
2793 arithmetic between values read by the parser has been removed
2794 * MAPLIB: improved precision of RMS & mean calculation
|
2795 fx 1.2 * $CINCL/{default,environ}.def: tidying and commenting
|
2796 fx 1.6 * protin.dic: updated and an alternative provided (VLdict.idl) from
2797 Victor Lamzin
|
2798 fx 1.4 * code for binary file transparency (as above)
|
2799 fx 1.2 * Lots of internal reorganisation
2800
2801 * Significant program bug fixes
|
2802 fx 1.4 * ABSURD: problems with `reindex'
2803 * AGROVATA: xloggraph o/p wrong; default INTENSITIES is PROFILE; changes if
2804 SCALE column present
2805 * ALMN: divide-by-0 errors
2806 * FFT: error for spacegroups P65 (and 61 ..); get Patterson SGs correct
2807 * FHSCAL: several corrections
2808 * HKLPLOT: spurious 'Disagreement between symmetry operators'; error in
|
2809 fx 1.2 multiplicity
|
2810 fx 1.4 * MLPHARE: fix divide-by-zero etc.
2811 * MTZ2VARIOUS: don't output excluded reflexions, treat formats as similarly
2812 as possible; output |FPH-FP| if FPH assigned; END not compulsory; output
2813 always to HKLOUT
2814 * OVERLAPMAP: fix problems of rounding errors in calc. of correlation coeff.
2815 * POLARRFN: failed to calculate rms value; put weighted RMS & mean
2816 into map header; correct sampling intervals in map header
2817 * PROLSQ: can no longer attempt to access hkl{in,out} (lcf files)
2818 * REINDEX: new version
2819 * ROTAPREP: takes DENZO input and madnes for050 files
2820 * ROTAVATA: confusion about FTWO/NOFTWO rejections between ROTAVATA and
2821 AGROVATA; change default on number of batches
2822 * SFALL: various small changes
2823 * VECREF: made consistent with FHSCAL (errors in them cancelled out)
2824 * WILSON: xloggraph plot
|
2825 fx 1.2
2826 * Significant program updates
|
2827 fx 1.4 * ABSCALE: new REINDEX option; changes for mosflm summed partials
|
2828 fx 1.2 * ABSURD: storage increase
|
2829 fx 1.4 * AGROVATA: accepts SCALE column etc.; redimensioned; ROGUES file extended;
|
2830 fx 1.6 changes for mosflm summed partials; negative values of SDADD
|
2831 fx 1.4 * ALMN: peak search changed, restored weighting of RMS & mean
2832 * CAD: fairly major re-write
2833 * COMPLETE: changes for triclinic data etc.
2834 * COORDCONV: was coord_conv
2835 * ECALC
2836 * EXTEND: new algorithm; MAPSYMMETRY option
2837 * F2MTZ: CTYP obligatory; FORMAT option
2838 * FFT, FFTBIG: EXCLUDE option; changes to default grid
2839 * LCF2MTZ: grok multi-record lcf files
|
2840 fx 1.6 * MLPHARE: various
|
2841 fx 1.4 * MTZDUMP: now as previous `dumpreso'
2842 * MTZUTILS: wasn't applying resolution cutoffs to output file
2843 * OVERLAPMAP: CHAIN option; change residue packing
|
2844 fx 1.2 * PDBSET: various extra options
2845 * PEAKMAX: keyworded and various other changes
|
2846 fx 1.4 * PROLSQ: new LIMIT keyword; various other changes
2847 * ROTAVATA: default INTENSITIES is PROFILE; changes for mosflm summed
2848 partials
2849 * SFALL: various changes
2850 * SURFACE
2851 * TRUNCATE: changes to interpolation etc.
|
2852 fx 1.6 * WATPEAK: includes contact list; carries through occupancy, B-factor info.
|
2853 fx 1.2
2854 [Changes to things in the `unsupported' directory not given here, although
2855 many have had some changes.]
2856
2857 * New programs
|
2858 fx 1.4 * ACT: analyse coordinates.
|
2859 fx 1.6 * AMORE: monolithic molecular replacement program.
|
2860 fx 1.2 * GENSYM: symmetry-related sites from atoms and list of vectors within
2861 defined volume
2862 * NPO: new version of PLUTO
2863 * PROCHECK system: stereochemistry checking
|
2864 fx 1.6 * RSPS: Patterson searching (previously aggregated)
|
2865 fx 1.2 * UNDUPL: essential for some data from Madnes (following Absurd).
2866 * VOLUME: polyhedral volume around selected atoms
2867
|
2868 fx 1.4 * Programs deleted or moved to the aggregated directories (with some
2869 suggestions for alternatives):
|
2870 fx 1.2
|
2871 fx 1.4 accsa, area [use areaimol], atconv, atomsf, atpeak [use watpeak], bavsc2,
|
2872 fx 1.6 brk2dia, brkmat, brksort [use procheck], burgess, cadpro, chelp, chkplt,
|
2873 fx 1.4 cli_help, convrnxp, coordswap, crossec, dabs, deg, diffop, dumpreso [use
2874 mtzdump], hlbgen, hlptree, limits [use pdbset or extend], mapbrick [frodo],
2875 mapcont [frodo], mapform [use mapexchange], minlim [use extend/pdbset],
2876 nadia [use angles/procheck], o2brk [O distribution (replaced by pdbset)],
2877 oscgen [with mosflm], patvec [use vectors], pdbrot [with ribbon], pltout
2878 [with ribbon], postplot [with ribbon], peaksearch [use peakmax], resection,
2879 reslicer, ribbon [aggregated], ribrot [with ribbon], rwbred, skewbrk, splitd
2880 [ribbon], symgen [use pdbset], tidytext, transz1, xplor2pdb [use pdbset],
2881 xyzlim, xyz_modify [use coordconv]
|
2882 fx 1.2
2883 * Housekeeping: (All?) the distributed files have been examined and only
2884 relevant ones should now be distributed. All the programs should now print
2885 version (date) information when they run.
|
2886 fx 1.5
2887 * Binaries will normally not be supplied on VMS tapes now. (We can't make AXP
2888 binaries anyway.)
|
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