1 fx 1.10 -*- mode: indented-text; fill-column: 78;-*-
2
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3 ccb 1.200.2.23 Summary of significant changes to CCP4 at version 6.1.24 ("")
4 ---------------------------------------------------------------------------
5
6 * Program changes:
7 * BUCCANEER: updated to 1.5
8 * POINTLESS: updated to 1.5.6
9
10 * Library changes:
11 * MMDB: updated to 1.23
12 * CCTBX: updated to
13
14 * Graphical User Interface:
15
16 * Bugs fixed:
17 * various build problems with shared libraries
18
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19 ccb 1.200.2.22 Summary of significant changes to CCP4 at version 6.1.13 ("Austwick")
|
20 ccb 1.200.2.21 ---------------------------------------------------------------------------
21
22 * Program changes:
|
23 ccb 1.200.2.22 * BUCCANEER: updated to 1.4
|
24 ccb 1.200.2.21
25 * Library changes:
26 * CLIPPER: update to 2.1
27
28 * Graphical User Interface:
29 * BUCCANEER_REFMAC: updated include cycling
30
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31 ccb 1.200.2.14 Summary of significant changes to CCP4 at version 6.1.3 ("No name")
32 ---------------------------------------------------------------------------
33
34 * Building etc.:
35 * gnu compiler 4.4 compliant
36 * supports Snow Leopard
37
38 * Program changes:
39 * IPMOSFLM: updated to 7.0.5
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40 fr45 1.200.2.19 * REFMAC: updated to 5.5.0109
41 * MOLREP: updated to 10.2.35
42 * SFCHECK: updated to 7.3.16
|
43 ccb 1.200.2.18 * POINTLESS: updated to 1.4.2
|
44 nds65 1.200.2.20 * CTRUNCATE: updated to 1.0.11
|
45 ccb 1.200.2.14
|
46 ccb 1.200.2.16 * Library changes:
47 * MMDB: update to 1.21
48
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49 ccb 1.200.2.14 * Graphical User Interface:
50 * IMOSFLM: updated to 1.03
51
52 * Bugs fixed:
53
54 * Known issues:
55 * 3488: IMOSFLM: cannot launch batch jobs from interface
56 * 3630: SCALEPACK2MTZ: does not read symmetry from input file
57 * 3894: DBhandles not python 3.0 compliant
58
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59 ccb 1.200.2.12 Summary of significant changes to CCP4 at version 6.1.2 ("Ingleborough")
|
60 ccb 1.200.2.10 ---------------------------------------------------------------------------
|
61 ccb 1.200.2.9
62 * Building etc.:
63 * ccp4.setup-dist renamed ccp4.setup-csh
|
64 ccb 1.200.2.12 * ccp4i, crank, imosflm launchers copied to bin directory during
65 installation
66 * csh no longer used during installation, all steps use sh
|
67 ccb 1.200.2.9
|
68 ccb 1.200.2.12 * Program changes:
|
69 ccb 1.200.2.10 * POINTLESS: updated to 1.3.9
|
70 nds65 1.200.2.13 * SCALA: updated to 3.3.15
|
71 ccb 1.200.2.12 * REFMAC5: updated to 5.5.0098. PHOUT added for building of MR solutions
72 with BUCCANEER
|
73 nds65 1.200.2.13 * MOLREP: updated to 10.2.31
74 * SFCHECK: updated to 7.3.13
|
75 nds65 1.200.2.11 * SIGMAA: new version from Ian Tickle
|
76 nds65 1.200.2.13 * OASIS: minor update
|
77 ccb 1.200.2.10
78 * Graphical User Interface:
79 * CRUNCH2: new interface for experimental phasing program
80 * CRANK: update to 1.3
|
81 ccb 1.200.2.12 * database back end off by default
82
83 * Bugs fixed:
84 * 3596: IMOSFLM: requires project directory to exist, fails otherwise
85 * 3689: POINTLESS loop variable overflow
86 * 3690: REFMAC5 interface not backwardly compatible
87 * 3713: REFMAC5 interface amplitude based twin refinement
88 * 3722: CTRUNCATE in import scaled task
89 * 3790: MOLREP multi-copy search failure
90 * 3797: all_load shared library builds under newer linux ld
91 * 3816: TLSANL anisotropic Us
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92 nds65 1.200.2.13 * various uninitialised variables caught
|
93 ccb 1.200.2.12
94 * Known issues:
95 * 3488: IMOSFLM: cannot launch batch jobs from interface
96 * 3630: SCALEPACK2MTZ: does not read symmetry from input file
97 * 3894: DBhandles not python 3.0 compliant
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98 ccb 1.200.2.9
|
99 ccb 1.200.2.7 Summary of significant changes to CCP4 at version 6.1.1 ("The New Inn")
|
100 ccb 1.200.2.6 ---------------------------------------------------------------------------
101
|
102 ccb 1.200.2.7 * Building etc.:
103 * intel 11: mostly supported
104
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105 ccb 1.200.2.6 * Program changes:
106 * PDB_EXTRACT: updated to 3.004
|
107 nds65 1.200.2.8 * REFMAC5: updated to 5.5.0072
|
108 ccb 1.200.2.7 * POINTLESS: updated to 1.3.1
|
109 nds65 1.200.2.8 * MOLREP: updated to 10.2.23
110 * SFCHECK: updated to 7.3.10
111 * CHAINSAW: accepts fasta alignment files
|
112 ccb 1.200.2.7
113 * Library changes:
114 * MMDB: update to 1.19
115 * monomer dictionaries: various updates, including CYS-MPR
116
117 * Updated interfaces:
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118 nds65 1.200.2.8 * REFMAC5: better integration of SAD refinement
|
119 ccb 1.200.2.7 * BP3: interface added
|
120 nds65 1.200.2.8 * TRUNCATE: CTRUNCATE options added
121 * DTREK2MTZ: CTRUNCATE now the default for intensity to SF conversion
122 * SCALEPACK2MTZ: CTRUNCATE now the default for intensity to SF conversion
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123 ccb 1.200.2.6
124 * Bugs fixed:
125 * 3628: ccp4i import task
|
126 ccb 1.200.2.7 * 3592: SFTOOLS interface
127 * 3619: REFMAC5 interface ignoring external file
128 * 3655: CHAINSAW not deleting CISPEP records from PDB
129 * 3656: PISA writing to $CCP4/share/pisa directory
130 * 3558: CAD segv
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131 ccb 1.200.2.6
132 * Known issues:
|
133 ccb 1.200.2.7 * 3488: IMOSFLM: cannot launch batch jobs from interface
134 * 3596: IMOSFLM: requires project directory to exist, fails otherwise
135 * 3630: SCALEPACK2MTZ: does not read symmetry from input file
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136 ccb 1.200.2.6
|
137 ccb 1.188 Summary of significant changes to CCP4 at version 6.1 ("Holy Trinity Church")
|
138 pjx 1.167 ---------------------------------------------------------------------------
|
139 pjx 1.148
140 * Building etc.:
|
141 ccb 1.199 * Refmac5.4+ requires a Fortran90 compiler, as do Molrep 10 and Sfcheck
142 7.3+. Configure tests for this, and disables refmac, molrep and sfcheck
143 builds if not found (e.g. if compiler is g77).
|
144 pjx 1.166 * ccp4.setup: the environment variable GFORTRAN_UNBUFFERED_ALL is
145 explicitly set to "Y" in the distributed setup files, to ensure that
146 the log file output from gfortran-compiled programs is written in
147 the correct sequence. This may incur a performance penalty however.
|
148 ccb 1.180 * POINTLESS, RAPPER, PISA optionally configured and built with core.
|
149 pjx 1.148
150 * Program changes:
|
151 pjx 1.173 * AREAIMOL: uses a new "spiral distribution" to divide up the surfaces
152 of the expanded Van der Waals atoms, which gives significant
153 improvements to the accuracy and stability of the accessible surface
|
154 pjx 1.176 area calculations - see the program documentation (Ian Tickle).
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155 mdw 1.156 * CAVENV: program now uses symmetry mates of input molecule unless
156 SYMM OFF set. Gives protein and solvent volumes within map limits.
|
157 nds65 1.200.2.5 * CRANK: updated to version 1.2.0. Greatly enhanced (Raj Pannu)
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158 ccb 1.200.2.3 * IMOSFLM: update imosflm to 1.0.0
|
159 pjx 1.162 * LOGGRAPH: is now able to give a basic view of the XMGR-style
160 normplot and correlplot output from SCALA, for systems where xmgr(ace)
161 is unavailable.
|
162 ccb 1.200.2.1 * MOLREP: updated to version 10.2.12.
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163 ccb 1.199 * MOSFLM: updated to version 7.0.4.
|
164 nds65 1.183 * OASIS: updated to OASIS-2006.
165 * PDBCUR: new option to delete ANISOU records.
166 * PDB_EXTRACT: updated to version 3.0 (since August 2007)
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167 pjx 1.164 * PDBSET: estimated molecular weight based on the sequence of residues
168 is automatically calculated when the SEQUENCE keyword is specified.
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169 ccb 1.198 * PHASER: updated to 2.1.4. This version covers MR, SAD and combined MR and SAD.
|
170 ccb 1.200.2.3 * REFMAC5: updated to version 5.5.0066. This adds twinned and anomalous
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171 ccb 1.198 refinement (Garib Murshudov, Raj Pannu, Pavol Skubak).
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172 ccb 1.200.2.3 * SCALA: updated to version 3.3.9
|
173 ccb 1.200.2.1 * SFCHECK: updated to version 7.3.7.
|
174 pjx 1.148
175 * Library changes:
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176 nds65 1.200.2.5 * Addition of a new "Diffraction Image" library which also comes with 4 small
177 jiffies installed in bin - diffdump, printpeaks, automask and diff2jpeg.
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178 ccb 1.189 * Monomer dictionary updated to 4.13
|
179 pjx 1.148
180 * New programs:
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181 ccb 1.188 * AFRO: multivariate substructure factor amplitude estimation for SAD/MAD
182 (Raj Pannu)
|
183 pjx 1.177 * BAUBLES/SMARTIE: new program for re-rendering CCP4 log files with
184 HTML markup (Peter Briggs & Kevin Cowtan).
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185 ccb 1.195 * BALBES: automated molecular replacement (Fei Long, Garib Murshudov,
|
186 nds65 1.200.2.5 Alexei Vagin).
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187 ccb 1.188 * cBUCCANEER: statistical model building, optimised for experimental
|
188 ccb 1.180 phasing. (Kevin Cowtan)
|
189 ccb 1.188 * CRUNCH2: direct mothod experimental phasing as part of CRANK (Jan
190 Abrahams)
|
191 nds65 1.183 * CTRUNCATE: New program for Intensity to Structure Factor conversion and
192 checking data quality (Norman Stein).
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193 pjx 1.191 * DBCCP4I: new database server for CCP4i, which includes a graphical
194 viewer for CCP4i projects plus other tools. (Wanjuan Yang & Peter Briggs)
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195 ccb 1.200.2.3 * IMOSFLM: imported imosflm 1.0.0
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196 rmk65 1.181 * MrBUMP: Automated molecular replacement, search model retrieval and
197 search model preparation for molecular replacement.
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198 pjx 1.151 * MTZ2CIF: new program for generating mmCIF reflection files suitable
199 for deposition, intended to replace OUTPUT CIF option of MTZ2VARIOUS.
200 See program documentation for more information. (Peter Briggs)
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201 ccb 1.200.2.3 * PARROT: automatic density modification and phase improvement (Kevin Cowtan)
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202 ccb 1.180 * PISA: the standalone version of the Protein Interfaces, Surfaces and
203 Assemblies server. (Eugene Krissinel) -- optional
|
204 nds65 1.200.2.5 * POINTLESS: Laue and Patterson group determination, v1.2.23. (Phil Evans)
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205 gwin 1.200 -- optional
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206 rmk65 1.181 * R500: new program for correcting REMARK 500 lines in PDB files.
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207 nds65 1.183 * RAPPER: conformer modelling through sampling residue rotameric states.
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208 ccb 1.180 (Nicholas Furnham, Paul de Bakker, Mark DePristo, Reshma Shetty,
209 Swanand Gore and Tom Blundell) -- optional
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210 ccb 1.188 * cSEQUINS: Statistical protein chain tracing (Kevin Cowtan)
|
211 pjx 1.163 * SEQWT: new utility to estimate protein molecular weight from the
212 sequence. (Eleanor Dodson)
|
213 pjx 1.159 * SYMCONV: new utility program for interrogating the CCP4 symmetry
214 libraries. (Peter Briggs)
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215 rmk65 1.181 * XIA2: Automated data reduction system designed to work from raw
216 diffraction data and a little metadata, and produce usefully reduced
217 data in a form suitable for immediately starting phasing and structure
218 solution.
|
219 pjx 1.148
220 * Graphical User Interface:
|
221 ccb 1.192 * Version 2.0
|
222 pjx 1.167 * Modules can now include "subfolders" of tasks to help with grouping
|
223 pjx 1.168 related tasks together within a module. These can also be included in
224 task packages that are exported - however developers should note that
225 packages created with subfolders are NOT backwardly compatible with
226 older versions of CCP4i.
|
227 pjx 1.165 * A right-mouse click on the job list presents a "context menu" offering
228 job manipulation options for the current selection (for example,
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229 pjx 1.166 rerun or delete jobs). Double-clicking with the left-mouse on a
230 specific job automatically tries to "rerun" that job.
|
231 pjx 1.175 * Options for customising the colours of jobs displayed in the job list
232 can be accessed via the "System Administration" and the context menu
233 described above.
|
234 pjx 1.166 * Viewing files from job in some cases (e.g. Refmac5) now also provides
235 options (when possible) to launch "plugin" applications (e.g. Coot,
236 CCP4mg) preloaded with the appropriate data.
|
237 pjx 1.160 * New option to re-import tasks that have already been installed in a
238 previous version of CCP4 (e.g. Arp/Warp): accessed via the
239 "Install/Uninstall Tasks" interface in the "System Administration"
240 menu. (Note that this function requires the user to have permissions
241 to write files to the CCP4i area.)
|
242 pjx 1.161 * ccp4ish can be run with a "-import_packages <old_ccp4>" option, which
243 attempts to automatically copy any tasks previously installed in the
244 CCP4 installation in <old_ccp4>, and add them to the current CCP4i
245 installation.
|
246 pjx 1.153 * Disabled ("greyed out") tasks can be enabled by setting the appropriate
247 option in the "Configure Interface" window
|
248 pjx 1.172 * MOSFLM-in-batch: now recognises keywords SYNCHROTRON POLARISATION,
249 DISPERSION and DIVERGENCE (used for data collected at a synchrotron)
250 and POSTREFinement keywords WIDTH, MOSADD and MOSSMOOTH.
|
251 ccb 1.200.2.3 * PARROT: new interface for the PARROT program.
|
252 pjx 1.154 * PISA webservice: the EBI Protein Interfaces Surfaces and Assemblies
253 webservice can be launched from the "Structure Analysis" and "Program
254 List" modules
|
255 nds65 1.183 * POINTLESS: new interface to the POINTLESS program (NB this supersedes
|
256 pjx 1.179 the prerelease interfaces: "Determine Laue Group", "Test Alternative
257 Indexing" and "Check Centre of Symmetry" - these interfaces can still
258 be accessed e.g. for reviewing old jobs, but are now deprecated).
|
259 pjx 1.152 * "SFs for Deposition" task (mtz2cif) now uses MTZ2CIF program rather
|
260 pjx 1.166 than MTZ2VARIOUS.
|
261 pjx 1.157 * GetMtzColumnResolution: new command that fetches the maximum and
262 minimum resolution limits for a specific column in an MTZ file.
|
263 pjx 1.169 * CURRENT_PROJECT and MG_CURRENT_PROJECT parameters are now stored in
264 status.def (previously in directories.def).
|
265 pjx 1.177 * XIA2: new interface to the XIA2 automated data processing package.
266 * Annotated HTML logfiles are generated after each program run using
267 the "baubles" program.
|
268 nds65 1.183 * Made a new task for job colourisation so it is more visible outside
269 the big configure task.
270 * Added Dyndom and Chooch interfaces files and added the tasks into
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271 fr45 1.178 Program list.
|
272 rmk65 1.181 * Added the MrBUMP (automated molecular replacement) interface.
|
273 nds65 1.183 * Added new Map & Mask Utilities task to calculate an omit map using
274 Sfcheck.
|
275 pjx 1.186 * Clipper Utilities: this module has been removed and the Clipper-based
276 tasks have been moved to other modules, mainly "Reflection Data
277 Utilities" and "Map & Mask Utilities".
|
278 fr45 1.190 * Added new interface for the existing getax program.
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279 pjx 1.196 * New task interfaces added to "Data Reduction" module ("Check Data
280 Quality" folder): "Analysis with ctruncate" and "Analysis with sfcheck"
281 allow experimental data to be characterised more easily.
282 * New task interface added to "Molecular Replacement" module ("Analysis"
283 folder): "Self RF with molrep" provides interface to the self-rotation
284 function calculation of Molrep.
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285 pjx 1.197 * autoSHARP: new interface to SHARP/autoSHARP. Needs a separate install
286 of SHARP/autoSHARP. (Clemens Vonrhein)
|
287 pjx 1.148
288 * Documentation:
|
289 pjx 1.149 * AREAIMOL: added figures to clarify the definitions of the different
290 surface types.
|
291 nds65 1.183 * MrBUMP: documentation for MrBUMP, automated molecular replacement
|
292 rmk65 1.181 program.
|
293 pjx 1.148
294 * Withdrawal:
|
295 mdw 1.174 * The following programs have been placed in deprecated/src for future
296 removal: BEAST (replaced by Phaser), ROTAPREP (replaced by Combat),
297 ARP_WATERS (use latest ARP/wARP), BPLOT, POLYPOSE, RSEARCH,
298 RESTRAIN.
299 * The following X-windows programs have been taken out of the build
300 procedure, prior to future removal: XLOGGRAPH (replaced by loggraph),
301 XDLMAPMAN, XDLDATAMAN, IPDISP (replaced by idiffdisp)
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302 pjx 1.148
303 * Examples:
|
304 ccb 1.200.2.2 * phaser_EP.exam: new example for Phaser 2.1.4, using a sulfur-SAD
|
305 mdw 1.174 dataset for bovine cubic insulin.
|
306 ccb 1.180 * pointless.exam: new examples for pointless
307 * rampage.exam: new example for rampage mode of rapper
|
308 ccb 1.192 * refmac_sad: new example for refmac SAD target function
|
309 gwin 1.200.2.4 * acorn: new example running from 1 Zn atom (Deuterolysin)
|
310 pjx 1.148
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311 mdw 1.132 Summary of significant changes to CCP4 at version 6.0
|
312 mdw 1.92 -----------------------------------------------------------
313
314 * Building etc.:
|
315 ccb 1.97 * Clipper/fftw built by default
|
316 mdw 1.101 * cctbx/phaser are included as separate packages. The main
|
317 pjx 1.121 CCP4 build will build them if these packages are included.
|
318 mdw 1.101 * There are a number of fixes for the AIX build.
|
319 pjx 1.103 * to_small_refmac.csh/to_big_refmac.csh: shell scripts to
320 reduce and restore the array sizes for Refmac5 prior to
321 compilation (in $CPROG/refmac5_/)
|
322 mdw 1.105 * A new ccp4.setup-zsh for ZSH users (Bill Scott)
|
323 mdw 1.142 * --with-x is now the default; use --disable-x if you have
324 problems with the X-windows build
|
325 pjx 1.145 * The script "patch_ccp4.sh" in $CETC can be used to
326 automatically download and apply available source code fixes
327 to the suite for UNIX-based systems. Note that any
328 recompilation must still be performed manually afterwards -
329 see Appendix M of the CCP4 installation instructions.
|
330 mdw 1.92
331 * Program changes:
|
332 mdw 1.141 * ANISOANL: now checks for non-positive-definite Us in XYZIN
333 and lists to log file (all options)
|
334 pjx 1.129 * AREAIMOL: new REPORT keyword allows control of output for
335 contact areas and reporting of area by residue
|
336 mdw 1.144 * CIF2MTZ: several new column labels added, including anomalous
|
337 mdw 1.101 * COORD_FORMAT: new keyword FIXBLANK
|
338 mdw 1.92 * DM: program now produces a data harvesting file
|
339 pjx 1.129 * MapSlicer: supports reading and display of mask files (new
340 "mask" mode); displays "greyscale" view superimposed on
341 contours; saves user preferences for contour levels and other
342 settings between sessions.
|
343 pjx 1.98 * MTZ2VARIOUS: if F(+) and F(-) are input for SHELX output then
344 rescaling is done within the program to produce
|
345 pjx 1.135 pseudo-intensities; OUTPUT CIF option updated to use tokens
346 from the PDB exchange dictionary for anomalous data and HL
347 coefficients.
|
348 mdw 1.101 * PDBCUR: new keywords SUMMARISE, DELHYDROGEN, MOSTPROB, CUTOCC,
|
349 pjx 1.121 and TRANSLATE (MDW)
|
350 pjx 1.171 * PDB_EXTRACT: new version 2.0
|
351 pjx 1.93 * PDBSET: new function ATRENUMBER (renumber atoms sequentially
352 without gaps in output file)
|
353 pjx 1.123 * PEAKMAX: new keyword EXCLUDE (turns suppression of peaks at the
354 edge of the map on or off)
|
355 mdw 1.142 * REFMAC: new version 5.2.0019
356 * MOLREP: new version 9.0.09
|
357 mdw 1.132 * MOSFLM: new version 6.2.5
|
358 mdw 1.142 * SFCHECK: new version 7.0.18
|
359 mdw 1.101 * SFTOOLS: new options LIST/SET DCELL/DWAVE for dataset information
|
360 ccb 1.126 * Matthews_coeff: outputs the Kantardjieff and Rupp resolution based
361 probabilities
|
362 fr45 1.112 * FFTBIG replaces FFT
363 * SCALEPACK2MTZ SYMM keyword not compulsory anymore, will try to pick up
364 spacegroup in the input file.
|
365 mdw 1.132 * TLSANL: ANISOU line in XYZOUT is now adjusted according to ISOOUT
366 keyword. Summary tags used to highlight important quantities.
|
367 mdw 1.92
368 * Library changes:
|
369 pjx 1.93 * CCPERR/ccperror: each time ccperror is called it invokes a
370 user-defined callback function which has previously been set
371 using new C library function "ccp4SetCallback".
|
372 mdw 1.101 * CCTBX library included as a separate package (Paul Adams,
|
373 pjx 1.121 Ralf Grosse-Kunstleve et al)
|
374 mdw 1.92
375 * New programs:
|
376 mdw 1.127 * BP3: multivariate likelihood substructure refinement and phasing
377 of S/MIR(AS) and/or S/MAD (Raj Pannu)
|
378 pjx 1.140 * CHAINSAW: new molecular replacement utility that mutates a pdb
379 file to poly-serine using a sequence alignment (Norman Stein)
380 * PDB_MERGE: jiffy to merge two PDB files (Martyn Winn)
381 * PHASER 1.3: molecular replacement (Randy Read et al)
|
382 mdw 1.143 * PIRATE (cpirate): statistical phase improvement (Kevin Cowtan)
|
383 pjx 1.140 * SUPERPOSE: secondary structure alignment (Eugene Krissinel)
|
384 mdw 1.92
385 * Graphical User Interface:
|
386 pjx 1.171 * Version 1.4.4.1
|
387 pjx 1.138 * AREAIMOL: new option to generate pairwise area differences for
388 "molecules" (defined as arbitrary groups of chains) in a PDB file.
|
389 mdw 1.101 * CRANK: interface to automated structure solution via experimental
|
390 pjx 1.104 phasing (currently SAD, SIR and SIRAS data)
|
391 pjx 1.108 * SHELX C/D/E: interface to running the SHELX C, D and E programs
392 standalone or as a pipeline in order to perform heavy atom
393 search and phasing
|
394 pjx 1.136 * CHAINSAW: interface to new program of the same name; mutates a pdb
395 file to poly-serine using a sequence alignment for molecular
396 replacement
|
397 pjx 1.171 * PISA webservice: the EBI Protein Interfaces Surfaces and Assemblies
398 webservice can be launched from the "Structure Analysis" and "Program
399 List" modules (added in 6.0.2)
|
400 pjx 1.120 * Scale and Merge Intensities (SCALA): option to output Scalepack
401 formatted reflection files suitable for input into SHELX or SOLVE
402 (corresponds to OUTPUT POLISH UNMERGED option of SCALA)
|
403 pjx 1.121 * Run Remote Jobs: option to use either rsh or ssh to run jobs on
404 remote machines.
|
405 pjx 1.124 * Output in different map formats: the interface should now only
406 offer output in the formats (O, QUANTA) that can actually be
407 created with the user's setup
|
408 pjx 1.116 * CreateLabinLine4: extended version of CreateLabinLine that allows
409 groups of up to four related labels to be specified, for example
|
410 pjx 1.146 H-L coefficients or F(+)/sigF(+) and F(-)/sigF(-) groups. This
411 command also supports a -command option similar to other
412 CreateLine-type commands. See the documentation for details.
|
413 pjx 1.96 * FindExecutable: new command, return full path of a program
414 executable
|
415 pjx 1.93 * Install Task: export task now allows save/restore of parameters;
|
416 pjx 1.121 tasks can be defined as basename/directory pairs; version number
417 included in archive filename.
|
418 pjx 1.93 * Logfile viewer: when viewing a long file, there is now the
419 option to look at the previous frame as well as the next one.
|
420 pjx 1.116 * MTZ handling: new commands GroupMtzCols, MtzColSameDataset,
421 GetMtzColType, GetMtzGroupByType.
|
422 pjx 1.93 * WarningMessage: has new options -image, -font and -color
423 * Superpose: when fitting atoms from one PDB file to another, atom
424 numbers given by the user now refer to those specified in the file
425 (rather than to the positions in the file)
|
426 pjx 1.104 * types.def: added new types "_res_file" (ShelxD result file) and
427 "_phs_file" (XtalView phases file)
|
428 pjx 1.121 * File Selection for Windows: drive can also be chosen from the file
429 browser.
|
430 pjx 1.107 * Disabled tasks: some task interfaces will be unavailable to users
431 if "prerequisites" (as defined in the taskname_prereq procedure in the
432 task interface file) are not found on the user's system.
433 "Disabled" means that the task button will be non-functional and the
|
434 pjx 1.113 text will be greyed-out.
435 Check the documentation $CCP4I_HELP/general/additional.html for
436 information on how to enable these tasks.
|
437 fr45 1.109 * Project Switching: Having a small menu button enabling to instantly
438 switch between projects without passing through "directories" interface
|
439 pjx 1.116 * Database search/sort: Having a new Button search/sort popping up a window
440 enabling users to do various kinds of simple/advanced search and/or sorting
441 also be able to refine sorts or searches.
|
442 pjx 1.137 * CreateToggleFrame: new option -justify allows programmer to specify the
443 positioning of the subframes (left, right or center).
|
444 mdw 1.92
445 * Documentation:
|
446 pjx 1.95 * Added documentation on adding doc comments for CCP4i core commands
447 ($CCP4I_HELP/progdocs/documenting.html)
|
448 pjx 1.117 * alternate_origins.html: updated with spacegroup numbers, information
449 about alternative settings and Hermann-Mauguin symbols
|
450 pjx 1.128 * Loggraphs: documentation for TABLE, GRAPHS, SCATTER etc now in
451 loggraphformat.html (see "File Formats" section)
|
452 mdw 1.92
453 * Withdrawal:
|
454 ccb 1.122 * fft (replaced by fftbig )
|
455 mdw 1.92
456 * Examples:
|
457 mdw 1.142 * abs, bp3, chainsaw, pdb_merge, phaser, pirate, superpose examples added
458 * New examples for using python interface to cctbx and phaser
459 (cctbx_py_test.exam and phaser_py_test.exam)
|
460 mdw 1.92
|
461 mdw 1.61 Summary of significant changes to CCP4 at version 5.0
462 -----------------------------------------------------
463
464 * Building etc.:
465 * configure: convex, stardent, titan, concentrix, ultrix and esv systems
466 all removed.
|
467 pjx 1.65 * Intel compilers: support for Intel compilers under Linux has been
468 implemented; use "configure linux_intel_compilers [options]"
|
469 ccb 1.72 * Intel compilers: support for Intel compilers under Linux on IA64
470 machines has been implemented (by SGI Japan); use "configure
|
471 ccb 1.82 ia64_linux_intel [options]"
|
472 ccb 1.72 * gnu compilers: IA64 support implemented; use "configure linux [options]"
|
473 pjx 1.75 (warning 3.0 broken)
|
474 ccb 1.83 * FreeBSD build: now can use g77 (thanks to Tim Gruene)
|
475 pjx 1.75 * LAPACK/BLAS: CCP4 configuration for NetLib BLAS and LAPACK now includes
476 all available functions (single, double, complex and double complex)
|
477 mdw 1.61
478 * Program changes:
|
479 pjx 1.63 * ACORN: updated version: 1) faster translation function using FFT (TRAN).
480 2) Phase errors can be calculated if true phases are input (LABIN).
|
481 mdw 1.61 * AMORE: substantially updated version: 1) Now estimates memory allocation
482 automatically (manual assignment is still available). 2) TABFUN: new
483 keyword BTARGET to adjust model B factors; NORMALISE keyword to generate
484 normalised model sf's. 3) CLMN: extended number of Bessel functions used
485 to generate spherical harmonics. 4) Fixes to Locked Rotation Function.
486 5) TRAFUN: can work with non-crystallographic translation.
|
487 pjx 1.63 * ASTEXVIEWER: please note updated conditions of use (see AstexViewer
488 documentation).
|
489 mdw 1.74 * BEAST: an MPI version has been added, see $CPROG/beast_/beast_MPI
|
490 pjx 1.77 * CAD: new keywords DRENAME, XNAME and DPNAME. SCALE keyword updated
491 to accept anisotropic B values.
|
492 mdw 1.70 * CIF2MTZ: new keyword NAME
|
493 mdw 1.88 * COMBAT: 1) new keyword NAME, 2) new option INPUT XDSASCII for reading
494 file XDS_ASCII.HKL from CORRECT stage of XDS
|
495 mdw 1.61 * COORDCONV: new option INPUT SNB reads SnB peaks files.
496 * DISTANG: changed format of symmetry/translational operators in logfile.
497 Note that the OUTPUT DISTOUT option must now be used to generate
498 output appropriate for input to WATERTIDY.
|
499 mdw 1.70 * DTREK2MTZ: new keywords NAME, WAVE (specifies wavelength of dataset).
500 * DTREK2SCALA: new keyword NAME
501 * F2MTZ: new keyword NAME
|
502 mdw 1.74 * FSEARCH: an MPI version has been added, see $CPROG/fsearch_mpi.f
|
503 mdw 1.61 * LSQKAB: increased array sizes (NATOM to 40000, NRS to 13999).
504 * MLPHARE: significant changes including:
505 1. ISOE/ANOE now taken (correctly) from last REFINEMENT cycle
506 2. Checks if two input sites are too close (prevents failures after
507 RANTAN/SHELX/ACORN if peak search puts a site close to its symmtery
508 related neighbour)
509 3. Checks if anom refinement is requested but all AOCC are zero; if
510 OCC is non-zero when only anomalous diffs are used.
|
511 pjx 1.71 * MAPSLICER/CCP4MAPWISH: 1) Default view changed to be "right-handed",
512 with option to chnage to "left-handed" view; 2) In "Harker" mode
513 axes are labelled "UVW" rather than "XYZ"; 3) new option to generate
514 contours starting from mean density in the map.
|
515 awa 1.73 * MOLREP: new version 7.5.01.
|
516 ccb 1.131 * MOSFLM: new version 6.2.5
|
517 pjx 1.62 * OASIS: new version 1.2.2.
|
518 pjx 1.66 * POLARRFN: new version extended to order 100 in sph. harm. expansion (from
519 Ian Tickle). This allows larger integration radius without loss of
520 resolution.
|
521 mdw 1.61 * PROFESSS: updated version outputs PDB file with the final atoms
|
522 pjx 1.68 * RASMOL: version 2.7.2.1.
|
523 mdw 1.70 * REBATCH: new BATCH XNAME keyword
524 * REFMAC: version 5.2.
|
525 pjx 1.62 * ROTAMER: updated version has for each Phe and Tyr rotamer Chi(1),Chi(2)
526 a symmetric one Chi(1),-Chi(2).
|
527 mdw 1.70 * RWCONTENTS: now uses residues from the monomer library: note that numbers
528 of hydrogens associated with CYS is now 4 (was 5), with HEM is 30 (was
529 17). Also, calculates I000 (square of atomic formfactors) from input
|
530 pjx 1.62 coordinates.
|
531 ccb 1.125 * SCALA: version 3.2.14
|
532 mdw 1.70 * SCALEPACK2MTZ: new keyword NAME
|
533 pjx 1.62 * SFALL: new keyword NAME
|
534 pjx 1.67 * SFCHECK: version 6.0.4
|
535 pjx 1.90 * SORTMTZ: new keyword VRSET.
|
536 mdw 1.61 * TRUNCATE: minor change to labels on cumulative intensity distribution
537 graph.
538 * WATERTIDY: no longer accepts the logfile output from DISTANG as input,
539 due to changes in DISTANG. Use the OUTPUT DISTOUT option of DISTANG
540 to prepare appropriate input for WATERTIDY.
541
542 * Library changes:
|
543 pjx 1.65 * New Core Libraries: new underlying C language libraries have been
544 introduced:
545 * CMTZLIB: MTZ file I/O and reflection data handling
546 * CMAPLIB: CCP4 mapfile I/O
547 * MMDB: Coordinate data handling (C++)
548 * CCP4_PARSER: CCP4 keyword parser
549 * CSYMLIB: CCP4 symmtery handling functions
550 * CCP4_GENERAL, CCP4_PROGRAM: utilities for providing CCP4 program
551 environment
552 * CCP4_ARRAY: resizeable array implementation
553 * CCP4_UNITCELL: utilities for manipulations based on cell parameters
554 * CVECMAT: vector and matrix manipulations
555 * LIBRARY_UTILS: general platform-independent utilies (date, filename
556 manipulations, etc)
557 * LIBRARY_FILE: general file I/O
558 * LIBRARY_ERR: functions for library error handling
559 These functions can be invoked from C/C++ applications (see e.g. NCONT,
560 PDBCUR, MTZDIFF). There are also a number of new C language libraries
561 providing Fortran interfaces:
562 * CCP4_DISKIO_F: Fortran API for file i/o
563 * CCP4_GENERAL_F: Fortran API to utilities providing CCP4 program
564 pjx 1.65 environment
565 * CCP4_UNITCELL_F: Fortran API to utilities for manipulations based
566 on cell parameters
567 * CCP4_PARSER_F: Fortran API for CCP4 keyword parser
568 * CMTZLIB_F: replicates old mtzlib.f
569 * CMAPLIB_F: replicates old maplib.f
570 * CSYMLIB_F: replicates old symlib.f
571 A number of old library files have been altered:
572 * ccplib.f: many functions replaced by CCP4_GENERAL_F
573 * library.c: withdrawn
574 * parser.f: many functions replaced by CCP4_PARSER_F
575 * rwbrook.f: withdrawn; replaced by Fortran API in MMDB
576 The Fortran APIs provided by the new libraries should match that from
577 the old (pre-5.0) libraries, and existing Fortran applications should be
578 unaffected by these changes.
579 The libraries build into three files: libccp4c (containing the core C
580 libraries in the first section above, except MMDB), libmmdb (containing
581 the MMDB libraries only), libccp4f (containing the Fortran and Fortran
582 API functions).
|
583 mdw 1.85 * Clipper: new C++ library for reflection and map handling (Kevin Cowtan)
|
584 pjx 1.87 * DNA_OUTPUT: library routines to support the DNA Project (see
585 http://www.dna.ac.uk/)
|
586 mdw 1.85 * FFTW: Fastest Fourier Transform in the West. Currently only used by
587 Clipper library.
|
588 mdw 1.70 * Monomer library: updated for REFMAC 5.2.
|
589 mdw 1.61
590 * New programs:
|
591 pjx 1.75 * BULK: bulk solvent correction for translation search and rigid body refinement
592 steps of AMoRe (A. Fokine, A. Urzhumtsev, G. Capitani, M.G. Grutter)
|
593 pjx 1.64 * DTREK2SCALA: convert integrated intensity and header files from D*TREK
594 into a multi-record mtz file (Gwyndaf Evans)
|
595 pjx 1.76 * EXTENDS: extend Fourier maps and compute standard uncertainty of electron
596 density (Phil Evans, Ian Tickle).
|
597 pjx 1.62 * MTZDIFF,MAPDIFF,PDBDIFF: utilities to examine differences between
598 pairs of MTZ, map and PDB files respectively (Peter Briggs)
|
599 mdw 1.80 * NCONT, PDBCUR and COORD_FORMAT: new coordinate utility programs based on the
|
600 pjx 1.62 MMDB library (Eugene Krissinel)
|
601 pjx 1.90 * PDB_EXTRACT 1.5: programs for extracting deposition data from logfiles
|
602 pjx 1.77 (RCSB)
|
603 mdw 1.78 * pdb-mode.el: major mode for editing Protein Data Bank files in
604 Emacs (Charlie Bond). There is also a simpler version pdb.el which
605 is mainly for highlighting (Martyn Winn). See also cif.el (Martyn Winn).
|
606 mdw 1.81 * TLSEXTRACT: a jiffy for extracting TLS parameters from the REMARK 3 records
607 of a PDB file (Jay Painter). Interfaced in Edit/Create TLS File.
|
608 pjx 1.66 * TOPDRAW: sketchpad for drawing topology cartoons of proteins
609 (Charlie Bond)
|
610 mdw 1.61
611 * Graphical User Interface:
|
612 pjx 1.89 * CCP4i version 1.3.18
|
613 pjx 1.62 * types.def: new widget types "varbutton", "postmenu", "selmenu",
614 "exframe_rb";
615 new file types "_MGPY_file" (molecular graphics script),
|
616 mdw 1.70 "_pickle_file" (MG save status), "_pic_file" (screen snapshot),
617 "_rlist_file" and "_sol_file" (Phaser solution files);
|
618 pjx 1.62 new MTZ label type "_mtz_label_e" (normalised structure factor).
|
619 pjx 1.75 * Help facilities: message line help is now also displayed as
620 "bubble help". Turn this feature off in "Configure Interface".
|
621 pjx 1.63 * Command templates (com files) can use ampersand ("&") as a
622 continuation character for both standard template lines and
623 LABELLINE commands.
|
624 pjx 1.62 * View Files from Job: when additional log and loggraph files are
625 output from a job, these are now grouped under submenus called
626 "Additional log files" and "Additional log graphs" (instead of
627 being in the main list of output files).
|
628 pjx 1.63 * Log file viewers: added option to use text browser to display
|
629 pjx 1.62 logfiles.
|
630 pjx 1.77 Up and down arrow keys enable single-line scrolling (Steven Ness).
|
631 mdw 1.61 * DbLockFilePid: returns pid which "owns" current database lock.
|
632 pjx 1.62 * CentreWindow: centres a window over a parent, or screen centre.
633 * MakeLock/LockStatus/DeleteLock/CreateLock: new procedures for
634 dealing with file locks.
|
635 pjx 1.86 * WriteImage: new command. Allows an image (any type supported by the
636 Tcl "image" command) to be displayed in a task interface.
|
637 pjx 1.66 * New module: "Graphics and Viewing Utilities" contains AstexViewer,
638 Loggraph, MapSlicer, RasMol (Unix only) and TopDraw.
|
639 pjx 1.62 * Amore: low resolution cutoff defaults to 15.0A, and is no longer
|
640 pjx 1.66 read from the input MTZ file. Solution files (.mr) include
641 SYMMETRY, CELL and RESOLUTION information in the header -
642 SYMMETRY from .mr file will be checked against that used for
643 Amore runs.
644 * Areaimol interface: new interface to calculate protein accessible
645 surface areas and area differences.
|
646 pjx 1.67 * ClustalW interface: new interface (nb the ClustalW program is not
647 distributed with CCP4).
648 * Data Harvesting Management Tool: new interface to review and
649 manage harvesting files produced from harvesting programs.
|
650 pjx 1.63 * Distang: removed from Program List, there is no dedicated Distang
651 task.
|
652 mdw 1.61 * Import Unscaled Data (combat): added option to enter wavelength.
653 * PrepHaData: SHELX options expanded to prepare data for either
654 SHELXS or SHELXD.
|
655 pjx 1.62 * Mlphare: output Hendrickson-Lattmann coefficients by default.
|
656 pjx 1.75 * Modeller: interface updated to work with either Modeller 6 (default)
657 or Modeller 4.
|
658 pjx 1.62 * MOSFLM interface: new interface to run MOSFLM in batch mode.
|
659 pjx 1.75 * Merge Monomer Libraries: a simpler interface has been implemented to
660 replace the old "AddDict" interface for merging monomer files.
661 "AddDict" can still be accessed via the Monomer Library Sketcher.
662 * Refmac5: substantial update to the Refmac interface.
|
663 pjx 1.63 * 'Old' Refmac/Protin: interfaces are retained to allow users to
664 review parameters from old jobs, but the tasks cannot be run as
665 the programs have been withdrawn.
|
666 pjx 1.62 * Scala: new option to accept observations previously flagged as
667 rejected by MOSFLM (ACCEPT keyword in SCALA program).
|
668 pjx 1.71 * Sketcher: 1) Report name of monomer and source file in sketcher
669 window; 2) Run imported CIF file through Libcheck automatically
|
670 pjx 1.75 * Edit/Create TLS File: now has "Reset" button to clear previously set
|
671 mdw 1.81 parameters. It can also extract TLS groups from the REMARK 3 records
672 of PDB format file. It will optionally handle TLS parameters.
|
673 mdw 1.61
674 * Documentation:
|
675 mdw 1.85 * symmetry.html, cheshirecell.html: new documents
|
676 pjx 1.62 * Sketcher: added to index of programs.
|
677 mdw 1.61
678 * Withdrawal:
679 * ABSURD, UNDUPL, MADLAT: programs for MADNES
680 * EXTEND: use MAPMASK
|
681 pjx 1.77 * REFORM: obsolete
|
682 mdw 1.61 * RWDICT: use MAKEDICT
683 * MSTAMP: obsolete
|
684 pjx 1.62 * PROTIN/REFMAC: use refmac5
|
685 mdw 1.61
686 * Examples:
|
687 mdw 1.70 * RNASE.PDB: naming of waters ("HOH") updated to be consistent with new
688 monomer dictionary, and with convention used in toxd.pdb: OW* changed
689 to O1, with one oxygen per "residue".
|
690 mdw 1.61
|
691 pjx 1.58 Summary of significant changes to CCP4 at version 4.2.1
692 -------------------------------------------------------
693
694 * Building etc.:
|
695 pjx 1.60 * General: running "make install" failed if executed immediately after
696 the configure step; now fixed.
|
697 pjx 1.58 * IRIX: fixed building of shared library by default on IRIX 6.5.
698 * OSF1: 1) new configure option --non_shared prevents linking executables
699 against shared libraries (including system libraries);
700 2) "-D__V40_OBJ_COMPAT -nointrinsics -D" compiler flags removed for
701 Tru64 V5.0.
702 * Mapslicer configuration: fixed problem with configure looking for Tk
703 library with the wrong file extension.
704
705 * Program changes:
706 * ASTEXVIEWER: .jar file updated to allow the viewer to run as
707 standalone.
708 * MOSFLM: version 6.2.2
|
709 pjx 1.59 contains fix for R/H3x problems.
|
710 pjx 1.58 * REFMAC5: version 5.1.24
711 * SCALA: version 3.1.9
712
713 * Library changes:
714 * CCIFLIB: fixed bug with passing fixed length for Fortran strings in
715 s/r ccp4ccif_setup_context.
716 * MAPLIB: five of the ENTRYs have been renames as they exceed 31
717 characters in length.
718 * PARSER: number of characters increased to prevent filename truncation
719 when filenames are read from the keyworded input.
720 * RWBROOK: fixed problem when spacegroup name is longer than space
721 permitted in PDB file.
722 * SYMLIB: increased the hashing parameter KPRI in CCP4_HASH_... routines
723 to 5003, to cope with maximum number of batches in SCALA (5000).
724
725 * Graphical User Interface:
726 * Version 1.3.8.
727 * General: Kill Job function updated to work under Mac-OSX and SunOS
728 * General: fixed problems starting help pages from KDE on Linux
729 * General: fixed problem with restarting task interfaces after being
730 closed using the Window Manager rather than the CCP4i "Close" button
731 pjx 1.58 * Refmac5: fixed problem with interface requesting harvesting information
732 in Review mode.
733 * Scala: new option to automatically combine all input datasets into
734 a single output dataset.
735 * Monomer Library Sketcher: 1) fixed problem with "unknown option -dash"
736 for Tk versions earlier than 8.3; 2) fixed problem with delocalised
737 and aromatic bond types not being written to bondlist.cif.
|
738 pjx 1.48
|
739 pjx 1.53 Summary of significant changes to CCP4 at version 4.2
740 ------------------------------------------------------
741
742 * Building etc.:
|
743 pjx 1.56 * IRIX 6.5: changed to n32 compilation.
|
744 pjx 1.53 * LAPACK: the BLAS and LAPACK libraries are now included in the CCP4
745 installation by default. If a suitable system-specific LAPACK library
746 is not found at configuration time then the version from Netlib will
747 be built. Use the --disable-lapack configure flag to suppress inclusion
748 of the LAPACK library, or the --with-netlib-lapack flag to force
749 building of the Netlib versions.
750 * configure: Have added an extra keyword --with-warnings. If this is not specified
|
751 ccb 1.54 some systems will be compiled with a -w which will suppress compiler warnings
|
752 pjx 1.53 for the main suite.
|
753 ccb 1.54 * xdlmapman: now builds using a m4 preprocessor stage to allow system
754 dependent FORTRAN file record sizes.
|
755 pjx 1.53
756 * Program changes:
757 * ALMN: automatically checks that input files have consistent indexing,
758 and suggests reindexing operation if they do not.
759 * AREAIMOL: calculates contact areas as well as ASA; allows large probe
760 sizes (up to 25A radius); new MATCHUP option for use with DIFFMODE
761 COMPARE e.g. for different confirmations; ignores hydrogens in input
762 files; improved handling of unknown atom types.
763 * ARP_WATERS: The CCP4-distributed version of arp_warp (v5.0) has been
764 renamed to "arp_waters". Example scripts, documentation etc has also
765 been renamed accordingly.
766 * BAVERAGE : htmlized the output.
767 * COMBAT: the MTZF option now accepts F(+) and F(-) as an alternative
768 to mean F. MISBATCH option removed: now only outputs batches which
769 are present in the input file. INPUT USER option fixed (was broken).
770 "I" decsriptors in FORMAT statements are automatically converted to
771 the appropriate "F" format. Fixed incorrect lattice type setting for
772 centred spacegroups in MTZ files.
773 * DTREK2MTZ: previously, handled files incorrectly if there was no
774 anomalous data - this feature now fixed.
775 * DYNDOM: New version 1.2
|
776 pjx 1.55 * ECALC: LABIN will now take DPH/SIGDPH, new MODD keyword.
|
777 pjx 1.53 * F2MTZ: for USER defined input, "I"'s in the Fortran FORMAT
778 statement are now automatically changed to the appropriate "F"
779 descriptors.
|
780 pjx 1.56 * FFFEAR: Upgrade to version 1.9
|
781 pjx 1.53 * FFT/FFTBIG: the default axis ordering is Z,X,Y for P1, monoclinic
782 space groups, and space groups 16, 17 and 18, and Y,X,Z for all
783 higher symmetry space groups. Default map volume in FFTBIG is now
784 always the whole unit cell.
785 * GENSYM: fix to SPHER ORTHOGONAL option.
786 * MATTHEWS_COEF: Added keyword AUTO that will produce a table
787 of the possible number of molecules in the Asym unit.
788 ** MOLREP: Molrep now uses keywords and command line options.
|
789 pjx 1.91 Also updated to verion 8.2.01.
|
790 mdw 1.57 * MOSFLM: version 6.2.1
|
791 pjx 1.53 * MTZ2VARIOUS: Added OUTPUT MAIN option.
792 * OASIS: new keywords RES and SIG, increased limit on number of
793 reflections, plus a number of bug fixes.
|
794 mdw 1.57 * REFMAC: version 5.1.19
|
795 pjx 1.53 * REVISE: Now produces graphs of the correlations between anomalous
796 differences for different wave lengths and the rms Dano; the
797 tables of ratioes of data sets split the data into 15 bins (was 10).
|
798 pjx 1.56 * SCALA: new version 3.1.4.
|
799 pjx 1.53
800 * Library:
801 * MAPLIB: Reinitialise mean and RMS density when creating multiple
802 maps in a single program run.
803 * PXXML: new subroutine library for writing XML.
804 * RWBROOK: s/r PDBREAD gives tries to identify ambigious atom names
805 like AC5* and NO4* when no element name is supplied.
806 * SYMOP: Hexagonal spacegroups 146, 148, 155, 160, 161, 166 and 167
807 are now refered to by the symbols H.
808 * unix.m4, vms.for, w32mvs.f: CCPOPN won't print error message for
809 file opening error if called with IFAIL=2.
|
810 ccb 1.54 * xdl_view: new version 4.5
|
811 pjx 1.53
812 * New programs:
|
813 ccb 1.54 * ABS: program to determine the hand of the heavy atom substructure
814 (Q.Hao)
|
815 pjx 1.53 * ACORN: ab initio procedure for the determination of protein structure
816 at atomic resolution (Yao Jia-Xing)
|
817 pjx 1.55 * ASTEXVIEWER: Java application for viewing proteins, ligands and electron
818 density maps (Mike Hartshorn)
|
819 pjx 1.53 * BEAST: Brute-force molecular replacement with Ensemble Average Statistics,
820 Maximum likelihood-based molecular repaclement (Randy Read)
821 * CIF2MTZ: program to convert mmCIF structure factors (e.g. from PDB)
822 to MTZ (Martyn Winn)
|
823 ccb 1.54 * FSEARCH: program to perform upto 6 dimensional molecular (envelope)
824 replacement search (Q.Hao)
|
825 pjx 1.53 * IAM (UNSUPPORTED): A specialised program for windows
826 purpose of this program is to just return the user name to std out
827 * PROFESSS (formally eleanorinabox): determination of NCS operators from
828 heavy atoms (Kevin Cowtan)
|
829 pjx 1.56 * REFINDEX: reindex dataset maximising correlation with reference dataset
830 (Ian Tickle). In Unsupported as only preliminary version.
831 * REFORIGIN: apply best origin shift to PDB atom co-ords according to
832 reference file (Ian Tickle). In Unsupported as only preliminary version.
|
833 ccb 1.54 * ROTAMER: list amino acids whose side chain torsion angles deviate from
834 Richardson's Penultimate Rotamer Library (Dirk Kostrewa)
835 * SAPI: heavy atom site location (Y.X.Gu, C.D.Zheng, H.F.Fan, Q.Hao)
|
836 pjx 1.53 * STGRID: modified version of STNET, produces a plot for measuring
837 the angular co-ordinates on a stereographic projection (Ian Tickle)
838 * TCL2HTML: Tcl script to convert Tcl script and CCP4i .def files to
839 html, with line numbering, colouring of comments, and html anchors
840 (Liz Potterton)
841
842 * Graphical User Interface:
|
843 pjx 1.56 * Version 1.3.7.
|
844 pjx 1.53 * Prepare HA data: includes option to apply high resolution cutoff
845 for MAD data (Revise RESO keyword). New option to input "native
846 data".
847 * FFT/PATTERSON tasks: upper sigma level now defaults to 100.
|
848 pjx 1.55 * New IMPORT/EDIT PROTEIN SEQUENCE task in Coordinate Utilities.
|
849 pjx 1.53 * MLPHARE task: new option to generate anomalous map. Don't allow
850 centric data only if anomalous difference data is used.
851 * REFMAC5: default for setting up restraints is now "do not check
852 anything".
853 * TRUNCATE: new option to input amplitudes (for analyses only).
854 * Tasks for importing data will now complain if you do not set a
855 project name or dataset name.
856 * Most tasks will get default title if you don't set one. When you
857 see how dull the default is, you will want to set your own.
858 * Selection behaviour for the job list in the main window has
859 changed: only last clicked item is selected. Selecting multiple items
860 is acheived by either ctrl-click (adds to selection) or shift-click
861 (add all items up to previously clicked line). Multiple items can
862 also be selected by clicking and dragging.
863 * Experimental Phasing module: "Merge datasets" task (CAD) added.
864 * MTZ label selection: the maximum length of menus of MTZ file labels is
865 now set in the "Configure Interface" window. Menus which have more than
866 this number of entries will be broken up into multiple columns.
867 * CreateLine command modified to:
868 1) Allow 'packing' of widgets into BLT table; 2) Use a different
869 naming scheme for widgets.
870 pjx 1.53 * Modules and Tasks: the list of modules and tasks is now read from a
871 modules.def file. Entries in an additional modules.def file placed in the
872 user's local area (e.g. $USER/.CCP4/unix/modules) will be appended to those
873 read from that in the main CCP4i area. The modules.def file can
874 be edited using the "Edit Modules File" task under the "System Admin" menu.
875 * Import Scaled Data: new task gives a single interface for importing data
876 from either Scalepack or D*trek - replaces the old Scalepack2mtz and
877 Dtrek2mtz tasks.
878 * OASIS: new task interface for phasing SIR or SAD data.
879 * ANISOANL, TLSANL: new task interfaces.
880 * modules_utils.tcl: new procedures to edit the modules.def files.
881 * Kill Job: modified to recursively kill all subprocesses of the script.
882 * Data Harvesting: the default is now to create harvesting files in the
883 current project directory, for tasks which support harvesting.
884 * PHISTATS: new task interface for phase set analyses.
885 * SFTOOLS: new option to generate Dano from F(+) and F(-).
886 * Main window: default size has been increased, so that all menu items
887 are visible on startup (the user can still resize it)
888 * AddOutputDir: new command to add a directory to the list of output "files"
889 from a job. The directory will not be displayed in the list of output files
890 but will be included in the cleanup procedure if the user deletes the job.
891 pjx 1.53 * SCALA: substantial changes for handling input and output datasets.
892 * CAD: new option to automatically check for and correct inconsistent
893 indexing between input files.
894 * XML: new xml_utils.tcl file contains procedures for handling CCP4 XML
895 files. Matthews and Molrep tasks will use XML to pass information
896 automatically if XML output is specified in preferences. NB these options
897 are developmental only.
898 * ARP/wARP: stand-alone interface has been withdrawn - get the latest ARP/wARP
899 suite and CCP4i interface from http://www.arp-warp.org/
900 * Mail CCP4: on Windows systems now calls up the CCP4 on-line help.
901 * Install New Task: substantially revised version allows install, uninstall and
902 export of new tasks. See documentation for full details.
903 * MAPCUTTING: new interface from Kevin Cowtan.
|
904 ccb 1.54 * DM: can specify NCS operators in a number of different ways (euler angles,
905 polar angle, rotation matrix or O matrix).
|
906 pjx 1.55 * WHATCHECK: new interface (Maria Turkenburg/Peter Briggs).
|
907 pjx 1.56 * File Viewers: user can set their default PDB and map viewer in Preferences.
908 * ROTAMER: new interface.
|
909 pjx 1.53
910 * Documentation:
911 * STNET: updated to clarify usage.
912 * CCP4i: extensive new documentation for all core Tcl routines.
913
914 * Withdrawal:
915
916 *
917
918 * Examples
|
919 pjx 1.56 * toxd.mtz, rnase18.mtz and rnase25.mtz now distributed as well as .na4 files.
|
920 pjx 1.53
|
921 pjx 1.48 Summary of significant changes to CCP4 at version 4.1
922 ------------------------------------------------------
923
924 * Building etc.:
925 * ccp4.setup: shouldn't add duplicated entries to the PATH variable.
926 * cif_mmdic.lib (binary version of mmCIF dictionary) now installed
927 in $CLIB rather than $CLIBD.
|
928 pjx 1.50 * configure: (i) updated for OSF1 V5.0. (ii) Always builds fsplit
929 automatically in bindir (defaults to $CBIN) and uses this in the build.
930 (iii) Use --with-lapack option to include LAPACK maths libraries in
931 build (see MODLIB documentation).
|
932 pjx 1.48
933 * Program changes:
934 * AMORE: sorts rotation function output for improved solutions.
|
935 ccb 1.52 * AREAIMOL: TRANS keyword - search extended from +/-1 lattice vectors to
936 +/2 vectors
|
937 pjx 1.48 * AXISSEARCH: updated output; now uses keyworded input
938 (see documentation).
939 * CAD: new keywords DCELL and DWAVELENGTH for adding/changing dataset cell
940 and wavelength attributes.
941 Applies temperature factor as part of scaling (via SCALE keyword).
942 * DM: version 2.1. Major changes are: NCS operators are now output as
943 Euler angles plus translations; program will calculate the value of
944 NMER automatically if it is omitted by the user; XtalView/O files
945 can be output to visualise the NCS elements.
|
946 ccb 1.52 * DYNDOM: no longer sensitive to the order of the atoms in the PDB file.
|
947 pjx 1.50 * F2MTZ: added summary tags to output.
|
948 pjx 1.48 * GENSYM: new keywords SORT (specifies order output for sites) and
949 CHAIN (assigns chain ids).
950 * GEOMCALC: prints out equations of fitted planes.
951 * IPDISP: revised version of ipdisp script; new spdfil for PX210
952 detector.
953 * MAPMASK: new XYZLIM MATCH option takes the output map limits from
954 a map supplied by the user.
955 * MAPROT: changes to CELL, GRID and SYMMETRY keywords (now have
956 WORK/XTAL subkeys), to AVERAGE keyword (change to format for entering
957 NCS operators) and new INVERT keyword. Option to cut density from
958 one map and transfer to another.
959 * MLPHARE: fixed DCYCLE REFCYCL option (was broken); substantial
960 reformatting of logfile output.
961 * PDBSET: new NOISE option adds random shifts to selected atom
962 coordinates. Checks that symmetry from SPACEGROUP is consistent
963 with that from input PDB file. Calculates fractional, as well as
964 orthogonal limits on coordinate set. New suboption FILE for
965 TRANSFORM keyword (see documentation). Chain selections now use
966 ChainId, if SegId is blank then SegId is always set to ChainID on
967 output.
968 * PEAKMAX: change of defaults, residue type for output set to HOH,
969 pjx 1.48 default atom name to O.
|
970 pjx 1.50 * PHISTATS: new SHIFT keyword applies a fractional shift to the second
971 phase set - useful if two phase sets refer to different crystal
972 origins.
973 * PROTIN: now can apply restraints from one residue to (a
974 symmetry-related copy of) itself.
|
975 pjx 1.48 * REBATCH: new CELL/WAVELENGTH keywords.
976 * REINDEX: new (optional) subkeywords HKL/AXIS for REINDEX keyword,
977 control how the transformations are supplied to the program.
|
978 ccb 1.52 * REVISE: new RESO keyword to set maximum resolution.
|
979 pjx 1.48 * RSPS: new version 4.2 from Stefan Knight.
|
980 pjx 1.50 * SCALA: new version 2.7.5.
|
981 pjx 1.48 * SCALEPACK2MTZ: added summary tags to output.
982 * SORTMTZ: change of defaults, residue type changed to HOH, atom
983 to O.
984 * TLSANL: many changes associated with new TLS option of refmac.
985
986 * Library:
987 * CCPLIB: CCPVRS prints 15 characters from program name (was 10).
988 CCPFYP recognises new command-line arguments -nohtml (suppress
989 output of html tags) and -nosummary (suppress output of summary
990 tags).
991 * FFFEAR_fraglib: library of representative protein fragments for FFFEAR.
992 * KEYPARSE: new entry ParseAtomSelect supports simple atom selection
993 commands.
994 * LAPACK: source code for BLAS and LAPACK packages included from
995 Netlib.
996 * MTZLIB: new DCELL and DWAVEL records in MTZ header for dataset-specific
997 cells and wavelengths. New routines LRIDC and LWIDC for read/write
998 dataset cell and wavelength info.
999 * MODLIB: a number of routines have been added to the library from
1000 various programs - see the MODLIB documentation.
1001 * PARSER: new routine RDATOMSELECT supports simple atom selection
1002 pjx 1.48 commands.
1003 * RWBROOK: s/r XYZOPEN checks for consistency between PDB defn.s of
1004 symmetry operations (taken from REMARK 290 lines, if present) and the
|
1005 pjx 1.49 order in $CLIBD/symop.lib or mtzlib. s/r SFREAD2 now correctly reads
1006 form factors for one character atom names from atomsf.lib (S, I and B
1007 were affected) (Clemens Vonrhein).
|
1008 pjx 1.48 * SYMLIB: s/r SYMFR2 now recognises real- and reciprocal-space
|
1009 ccb 1.52 axis vector operations, e.g. a*+c*,c*,-b*; new s/r SETLIM_ARP
1010 returns the ARP asu limits.
|
1011 pjx 1.48 * SYMOP.LIB: fixed point groups for alternate spacegroups 1003, 1004,
1012 1005, 2005, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015.
|
1013 pjx 1.51 * XDL_VIEW: new version 4.4
|
1014 pjx 1.48
1015 * New programs:
1016 * ANISOANL: various analyses of model anisotropic U values (Martyn Winn)
1017 * ccp4keys: awk script for extracting keywords form a log file in a format
1018 which can be cut and pasted into a new command file. (Kevin Cowtan)
1019 * CAVENV: Calculates cavities in macromolecular structures (Anne Volbeda)
1020 * CCP4MAPWISH: customised wish interpreter required for MAPSLICER. (Peter Briggs)
1021 * COMBAT: replacement for ROTAPREP. (Alun Ashton)
1022 * DTREK2MTZ: converts d*trek scalemerge output into MTZ format. (Jim Pflugrath)
1023 * FFFEAR 1.2: Fast Fourier FEAture Recognition program. (Kevin Cowtan)
1024 * FFJOIN: joins together fragments from FFFEAR. (Kevin Cowtan)
1025 * MAP2FS: jiffy to convert CCP4 maps/masks to XtalView fsfour format. (Kevin Cowtan)
1026 * MAPSLICER: viewer for contoured sections through CCP4 maps. (Peter Briggs)
1027 * MOSFLM: now distributed with CCP4. (Andrew Leslie / Harry Powell)
1028 * REFMAC5: major new version of REFMAC (Garib Murshudov). Old refmac and
1029 protin moved to unsupported.
1030 * ROTGEN: Simulate X-ray diffraction rotation images. (John Campbell)
|
1031 pjx 1.51
1032 * Graphical User Interface:
1033 * Installation: CCP4i no longer requires Tcl/Tk to be built with a non-default
1034 flag. It is best run using the bltwish interpreter.
1035 * Monomer Library Sketcher: for graphics display of monomers, and
1036 interface to Libcheck and the monomer geometry libraries.
1037 * New interfaces to BAVERAGE, CONTACT, FFFEAR, DMMULTI,
1038 DTREK2MTZ, SFTOOLS for SF analysis, SIGMAA, and WATERTIDY.
|
1039 pjx 1.48
1040 * Documentation:
1041 * alternate_origins: lists alternate origins for different spacegroups.
1042 * lsqkab.html: added a "known problems" section.
1043 * symlib.html: extended section on applying symmetry operations.
1044
1045 * Withdrawal:
1046
1047 * ROTAPREP: moved to unsupported.
1048
1049 * Examples
1050 * axissearch.exam: updated for revised version of AXISSEARCH.
1051 * toxd.pdb: waters renamed to HOH O1.
|
1052 pjx 1.49 * run-all: testing script in $CEXAM/unix/runnable which will
1053 run all examples and report any failures
|
1054 pjx 1.48 * tutorial2000: ccp4i-based tutorials. Old tutorials removed since
1055 getting out of date.
1056
|
1057 mdw 1.44 Summary of significant changes to CCP4 at version 4.0
1058 ------------------------------------------------------
1059
1060 * Building etc.:
|
1061 mdw 1.47 * configure: new options --help, --with-rxdispencer and --disable-ccif
1062 New system linux_compaq_compilers
|
1063 mdw 1.44 * etc/GFAC2PDB.COM added for VMS
1064 * include/ccp4.setup-dist and ccp4.setup-bash: CCP4_OPEN set to
1065 UNKNOWN by default since necessary for some programs, and this
1066 is common practice. Beware over-writing existing files!
|
1067 mdw 1.46 * lib/data: running fontpack has been moved to "make install" step,
1068 since if a shared library is used it needs it to have been installed.
|
1069 mdw 1.44
1070 * Program changes:
|
1071 mdw 1.46 * AMORE: major new version from Jorge Navaza
|
1072 mdw 1.44 * AREAIMOL: default MODE is now NOHOH. Attempts to identify isolated
1073 areas of surface (eg cavities) in MODEs NOHOH and ALL.
1074 * ARP_WARP: ARP/wARP v5.0 - replaces "arpp".
1075 * CONTACT: broken MODE ISUB fixed. CRYST1/SCALE cards not required except
1076 for MODEs AUTO and IMOL. New keyword BIGSEARCH allows larger volume to
1077 be searched for contacts under MODE AUTO. Should correctly identify H32
1078 and R32.
|
1079 mdw 1.47 * COORDCONV: extended to read *.ha format files.
|
1080 mdw 1.44 * DETWIN: LABIN keyword added - program now accepts F's and I(+/-).
1081 Performs new tests for twinning as a function of twinning fraction and
1082 resolution - see documentation. OPERATOR keyword replaces existing
1083 SYMMETRY keyword (which is still valid).
|
1084 mdw 1.46 * DM: version 2.0.5.
|
1085 pjx 1.48 * FHSCAL: can now apply scales calculated for F's to F(+), F(-), Imean,
1086 I(+) and I(-), and warns if not all scalable members of a dataset have
1087 scales applied. AUTO option enables automatic selection of all
1088 scalable columns in chosen datasets.
|
1089 mdw 1.44 * IPDISP: new version and new spdfils for reading packed MAR image files.
1090 * MAPDUMP: accepts END/RUN/GO keyword as well as end-of-file.
1091 * MLPHARE: keyword COORDS writes heavy atom coordinates to pseudo-pdb file.
1092 * MTZ2VARIOUS: Extra LABIN columns FPART_BULK_S and PHIPART_BULK_S for
1093 CIF output.
1094 * MTZMADMOD: labels changed so that +/- are now (+)/(-)
1095 * NCSMASK: new SPACING subkeyword for GRID option, to set arbitrary grid
1096 spacing.
1097 * PDBSET: added OCCUPANCY RESET and EXCLUDE SIDE options. Fixed broken
|
1098 mdw 1.47 TRANSFORM FRACTIONAL option. New EXCLUDE WAT/HOH option.
|
1099 mdw 1.44 * PREPFORM, PREPSHEL: new version as part of ARP/wARP suite v5.0.
1100 * PROTIN: redimensioned for ARP/wARP.
1101 * RWCONTENTS: keyword NHOH added to estimate no. of water molecules
1102 that can be found by PX (Carugo and Bordo).
1103 * REBATCH: A new sub keyword to BATCH, MAXWIDTH, has been added to specify
1104 the maximum width of reflections. Those with higher widths are rejected.
|
1105 mdw 1.47 * SCALA: new version 2.7.2.
|
1106 mdw 1.44 * SCALEIT: can now apply scales calculated for F's to F(+), F(-), Imean,
1107 I(+) and I(-), and warns if not all scalable members of a dataset have
|
1108 mdw 1.47 scales applied. AUTO option enables automatic selection of all
1109 scalable columns in chosen datasets.
|
1110 mdw 1.44 * SCALEPACK2MTZ: Added code to insert html tags in log files.
1111 * SFCHECK: version 5.3.4
1112 * SORTMTZ: Added code to insert html tags in log files.
1113 * SURFACE: prints out total accessible area after each calculation.
1114 * TLSANL: New keyword BINPUT to specify whether Bs or Us in XYZIN.
1115 * TOPP: topp.f, autosnd.f, toplist.f - all leading tabs changed to spaces
1116 for compilation on AIX. Now version 6.5
1117 * TRUNCATE: new loggraph table of centric and acentric moments for identifying
1118 twinning. Plots of F/sigma added to falloff plots for identifying anisotropy.
1119 Code added to check if data is anisotropic. Included a new keyword SCALE that
1120 when provided overrides the wilson plot scale. Added code to insert html tags
1121 in log files.
1122 * WATERTIDY: fixed faulty oxygen atom recognition.
1123 * WATNCS: all leading tabs changed to spaces for compilation on AIX.
1124
1125 * Library:
1126 * lib/ccif: Peter Keller's ccif library for handling mmCIF
1127 * cciflib.f: new library for handling mmCIF coordinate files. At present,
1128 not used by distributed programs. Uses libccif.a
1129 * harvlib.f: new library for writing data harvesting files. Used by
1130 MLPHARE, TRUNCATE and RESTRAIN. Uses libccif.a
1131 mdw 1.44 * lgglib.f: all leading tabs changed to spaces for compilation on AIX.
1132 * rwbrook.f: new routine NUM_EXPECTED_WATERS. Changes to XYZOPEN (issues
1133 warnings if no CRYST1 or SCALE cards are found in input PDB file).
|
1134 mdw 1.45 * sc_radii.lib: atomic radii library file for new SC program.
1135 * symlib.f: new s/r CALC_ORIG_PS.
1136 * symop.lib: one line per symmetry operation. Some minor corrections.
|
1137 mdw 1.44
1138 * New programs:
1139 * MOLREP: automated program for molecular replacement, from Alexei Vagin
1140 * OASIS: program for breaking phase ambiguity in OAS or SIR, from Quan Hao
1141 * RWCONTENTS: promoted from unsupported.
1142 * SC: program to analyse shape complementarity of molecular interfaces
1143 * T_SHIFT: part of ARP/wARP suite v5.0.
1144
1145 * Documentation:
|
1146 mdw 1.46 * ccplib.html: new documentation for the CCP4 utility routines in CCPLIB.
1147 * diskio.html: new documentation for the I/O library routines in DISKIO.
|
1148 mdw 1.44 * INDEX.html: new File Formats section. Includes pdbformat.html taken
1149 from original rwbrook.html, and mmcifformat.html for mmCIF and CCIF.
1150 Descriptions of MTZ and map formats can be found in Library section.
|
1151 mdw 1.46 * keyparse.html: new documentation for the KEYPARSE library routines.
1152 * library.html: new documentation for the routines in LIBRARY.C.
|
1153 mdw 1.44 * makedict.html: now has hints for making PROTIN dictionary entries.
1154 * modlib.html : new documentation for the CCP4 maths routines library
1155 MODLIB.
|
1156 mdw 1.46 * parser.html: new documentation for the PARSER library routines.
1157 * unix.html: documentation for the library routines in UNIX.M4, VMS.FOR and
1158 W32MVS.
|
1159 mdw 1.44
1160 * Withdrawal:
1161
1162
1163 * Examples
1164 * arp_warp.exam: updated version of old "arpp.exam" using ARP/wARP v5.0
|
1165 mdw 1.46 * cad_rnase.exam: example using CAD to add project and dataset
1166 information to an mtz file.
|
1167 mdw 1.44 * makedict.exam: two examples of using MAKEDICT.
|
1168 mdw 1.46 * mtzMADmod.exam: example of adding F+/- columns to a file.
|
1169 mdw 1.44 * oasis_oas.exam, oasis_sir.exam: two examples for OASIS.
1170 * protin_substrate: updated to use MAKEDICT.
1171 * rebatch.exam: A new example using the aucn data.
1172 * rnase.pdb: terminal oxygens renamed from "OE" to "OXT",
1173 in line with the PDB standard.
|
1174 mdw 1.45 * sc.exam: two non-runnable examples for SC.
|
1175 mdw 1.46 * sfall.exam: three simple examples of running SFALL.
1176 * surface_rnase.exam: example of running SURFACE on rnase data.
|
1177 mdw 1.44 * toxd.pdb: terminal oxygen renamed from "OE" to "OXT",
1178 in line with the PDB standard.
1179
|
1180 mdw 1.40 Summary of significant changes to CCP4 at version 3.5
1181 ------------------------------------------------------
1182
1183 * Building etc.:
1184 ** configure script has new system irix64 for 64 bit compilation on
1185 SGI with irix 6.*
1186 ** configure script has new option --with-x for sgi/linux/and osf1
1187 will compile the xwindows progs
1188 ** ccp4.setup-dist/bash : has PLOT_COMMAND and PRINT_COMMAND that need
1189 to be set for XCCPJIFFY's to work correctly.
1190 * duptree: new version using relative pathnames. Original behaviour can
1191 be obtained by using the -a (absolute pathname) flag.
1192 * Makefile.in in $CCP4 has new JAVATARGETS target, currently only used
1193 for moving java executables JLogGraph.class and JLogCanvas.class from
1194 $CPROG to $CBIN upon "make install".
1195 * x-windows/XCCPJIFFY: added IRIX_6 option (actually the same as IRIX_5
1196 but clearer to have it explicit)
1197 Irix 6.5 needed a section to itself.
1198 ** x-windows/XCCPJIFFY: added Imakefile.in
1199
1200
1201 mdw 1.40 * Program changes:
1202 * AREAIMOL: substantially updated version now also incorporates DIFFAREA,
1203 RESAREA and WATERAREA. See documentation.
1204 * CAD: new keywords PNAME/DNAME for adding dataset info. Will now swap
1205 F+/F- or I+/I- columns on changing hand of indices.
1206 * CONTACT: substantially new version.
1207 * DM: Version 2.0.3
1208 Output log file enhanced if viewed through web browser.
1209 * ECALC: now uses absolute differences to calculate E. EXCLUDE keyword
1210 added. Extra column SIGE written to output mtz. Scatter Plot removed
1211 from the log as the info is already in the tables.
1212 * FFT,FFTBIG: XYZLIM ASU option automatically sets map limits to correct
1213 asymmetric unit.
|
1214 mdw 1.43 * FHSCAL: Modification from Richard Kingston to process F+/- columns.
|
1215 mdw 1.40 * FREERFLAG: New keyword SEED to seed random number generator using
1216 current time. Systematic absences also assigned a FreeR flag (no longer
1217 flagged as missing). OLDFREE keyword removed.
1218 * HKLVIEW: new -d option specifies resolution limit.
1219 * ICOEFL: LABOUT and END keywords fixed.
1220 * IPDISP: extra spdfil files added for new detectors. Some options
1221 for existing detectors updated.
1222 * MAPMASK: SYMM now over-rides map file header. Optional MODE keyword
1223 added.
1224 * MTZ2VARIOUS: OUTPUT CIF now gives correct spacegroup format. OUTPUT
1225 CNS and OUTPUT SCAL (for SOLVE) added.
1226 * MTZDUMP: limits output in "resolution" column have been corrected.
1227 * NPO: subkeyword FRAC added to existing SECTNS keyword.
|
1228 mdw 1.43 * PDBSET: SPACEGROUP and EXCLUDE HEADER options fixed.
|
1229 mdw 1.40 * PEAKMAX: New output option FRAC added. Existing output PEAKS option now
1230 writes to logical name PEAKS. Program now outputs the height/rms(density)
1231 (instead of height) in output files and in logfile. Some formats changed
1232 in logfile and OUTPUT BROOKHAVEN.
1233 * PROTIN: fixed problems with being unable to assign a SPECial distance
1234 between atoms in multiple confirmations, and with checks only for
1235 distances being applied for first residue of non-protein chains.
1236 * REFMAC: version 4.0.2 with anisotropic refinement
1237 * REINDEX: new version - see documentation.
1238 * ROTAPREP: option SCAL_NM2 for new SCALEPACK output.
1239 * RSTATS: functionality of RESOLUTION keyword changed. All reflections
1240 now written to output mtz.
1241 * RWCONTENTS: extended to give estimates of the fraction of the unit cell
1242 which is empty or which contains solvent. Also calculates Matthews
1243 coefficient.
1244 * SCALA: new version 2.5.5.
|
1245 mdw 1.41 Output log file enhanced if viewed through web browser.
|
1246 mdw 1.40 * SCALEIT: SCAT keyword to include scatter plots in log files. Default
1247 is now not to.
1248 * WILSON: can read in intensities or amplitudes.
1249
1250 * Library:
1251 * lgglib.f: routines from Guoguang Lu
1252 * libhtml.f: new library routines for adding HTML tags into program output
1253 so that log files can be viewed as HTML documents. Associated java code in
1254 JLogGraph.java (compiled as JLogGraph.class and JLogCanvas.class) allow
1255 log graphs to be embedded and viewed directly through Java-enabled HTML
1256 browser.
1257 * library.c: new routine hgetlimits for harvesting
1258 * maplib.f: descriptive names for subroutines now available alongside existing
1259 subroutine names. New routines CCP4MAPHEAD, CCP4MAPIN and CCP4MAPOUT added.
1260 * modlib.f: new matrix multiplication routines MATMULNM and MATMULGEN.
1261 * protin.dic: IUM residue entry revised with more comprehensive list of elements.
1262 * rwbrook.f: routines XYZADVANCE and WBCELL now print spacegroup name (if available)
1263 after cell info of CRYST1 card. New routine WBSPGRP used to set spacegroup name.
|
1264 mdw 1.43 RBSPGRP now returns spacegroup name automatically left-justified. New routine
1265 RWNOHEAD suppresses output of CRYST1 and SCALE cards.
|
1266 mdw 1.40 * symop.lib: extended version of symop.lib, containing additional alternative
1267 spacegroup names. Groups 1017, 2017, 2018, 3018 added. (Old symop.lib
1268 retained in symop_old.lib)
1269 * symlib.f: new routine MSYMLB2 to return CIF-style spacegroup name. New routine
1270 MSYMLB3 returns most detailed spacegroup name, checks all symmetry operators
1271 in spacegroup form a closed set, and derives the pointgroup from the existing
1272 subroutine PGDEFN (ignoring that given in $SYMOP). New routine SYMTR4 converts
1273 matrices to symmetry operations more consistently than existing SYMTR3.
1274 Routines SETUP, LOOKUP and ZEROIT renamed (now preceeded by "CCP4_HASH_"), and
1275 relevant programs altered (POSTREF, REBATCH, SCALA).
1276 * $CLIBD/protin.dic: HOH added as residue to fit pdb format
1277
1278 * New programs:
|
1279 mdw 1.42 * DETWIN: detwins merohedrally twinned data.
|
1280 mdw 1.40 * DYNDOM: Program to Determine Domains, Hinge Axes and Hinge Bending Residues
1281 in Proteins where Two Conformations are Available. From Steve Hayward.
1282 * FINDNCS: detect NCS operations automatically from heavy atom sites.
1283 From Guoguang Lu.
1284 * MTZMADMOD: Jiffy for converting between F+/F- and F/D
1285 * TOPP: an automatic topological and atomic comparison program for protein
1286 structures. From Guoguang Lu.
1287 * WATNCS: Pick waters which follow NCS and sort out to NCS asymmetric unit.
1288 From Guoguang Lu.
1289
1290 * Documentation:
1291 * ipdisp.html: contains list of available spdfils and new section on creating
1292 and custominsing spdfils.
1293 * libhtml.html: documentation for new libhtml.f library subroutines.
1294 * protin.html: contains example with RNA.
1295 * symlib.html: documentation for symmetry library subroutines in symlib.f.
1296 * freerunique.html, reindexing.html, scalechoose.html, twinning.html: new
1297 general documentation.
1298
1299 * Withdrawal:
1300 * DIFFAREA, RESAREA and WATERAREA all now incorporated into AREAIMOL.
1301 mdw 1.40
1302 * Examples
1303 * areaimol.exam: examples for new version.
1304 * toxd.pdb: Chain names added and TER card at end of protein
1305 * ncsmask.exam: one run of pdbset removed as toxd.pdb now has chain ID
1306 * arpp.exam: pdbset run ajusted. extend replaced with mapmask.
1307 * watpeak.exam: pdbset run ajusted.
1308 * watertidy-3shells: pdbset run ajusted.
1309 * sortwater.exam: pdbset run removed.
1310 * bplot.exam: resudue names changed to include CHAIN ID.
1311 * f2mtz.exam: adjusted XPLOR example to accept output from new mtz2various.
1312 new example added.
1313 * mtz2various.exam: extra example of OUTPUT USER with DUM labels.
1314 ** rnase : $CEXAM/rnase/ directory added with data/scripts/pdb
1315 see $CEXAM/rnase/README for details
1316
1317
|
1318 mdw 1.38 Summary of significant changes to CCP4 at version 3.4
1319 ------------------------------------------------------
1320
1321 * Building etc.:
1322 * duptree: new script for setting up multiple installations
1323 * C programs: changes to PLTDEV, BINSORT and SOLOMON so that they should
1324 compile on HPUX.
1325 * linux/g77: all programs should now compile with linux/g77
|
1326 awa 1.39 * x-windows: trial configure and Makefile.in for IRIX, OSF1 and LINUX.
|
1327 mdw 1.38
1328 * Program changes:
1329 * AREAIMOL: now takes keyworded input.
1330 * FFT/FFTBIG: will now print out Harker sections.
|
1331 awa 1.39 * GETAX: New version - g77 compliant.
|
1332 mdw 1.38 * NPO: now can take XYZIN again! New version from Eleanor Dodson.
|
1333 awa 1.39 * PROCHECK: New version - now g77 friendly.
|
1334 mdw 1.38 * SCALA: version 2.4.2 included
1335 * SIGMAA: subsubkeywords LOW and HIGH of COMB RESO removed, since
1336 of little use and didn't work properly.
1337 * SORTWATER: Duplicate waters (after applying symmetry operators) are removed.
1338 * TRUNCATE: FALLOFF option to visualise anisotropy (Yorgo Modis).
1339 * VECTORS: now sets Bfactors to 1.0 to fit in with NPO
1340
1341 * Library:
1342 * ccplib: minor y2k fixes.
1343 * rwbrook: new routines RBRORF2, CVANISOU, RBSPGRP.
1344 * symlib: changes to SYMTR3 to allow calculation of Harker sections,
1345 new ENTRY CENTPHS to return PHASE class.
1346
1347 * New programs:
1348 * BAVERAGE: promoted from Unsupported (now keyworded).
1349 * BPLOT: promoted from Unsupported.
1350 * MAPDUMP: from old unsupported PRMAP.
1351 * RANTAN: Direct Method module for the determination of heavy atom positions
1352 in a macro-molecule structure or to determine a small molecule structure.
1353 * SFCHECK: Structure factor checking
1354 * SFTOOLS: Reflection data file utility program from Bart Hazes.
1355 mdw 1.38 * DMMULTI: multi-xtal density modification package
1356
1357 * Documentation:
1358 * html versions of dm_ncs_averaging and dm_skeletonisation added.
1359 * arppdoc.ps removed - contents included in arpp.html
1360 * $CCP4/manual/procheck/manual.ps removed since out-of-date. New
1361 comprehensive html version.
1362
1363 * Withdrawal:
1364 * ABSCALE: obsolete
1365 * AGROVATA/ROTAVATA: replaced by SCALA
1366 * ENVELOPE: replaced by DM
1367 * EXTEND: moved to unsupported, replaced by MAPMASK.
1368 * FLATMAP: replaced by DM
1369 * PROLSQ: replaced by REFMAC
1370 * PSAVER: replaced by NCSMASK/DM.
1371 * RESLICE: replaced by MAPMASK.
1372
1373
|
1374 mdw 1.37 Summary of significant changes to CCP4 at version 3.3
1375 ------------------------------------------------------
1376
1377 * Building etc.:
1378 * $CCP4/Makefile.in: makeman script automatically runs when typing make
1379 from $CCP4.
1380 * $CHTML/makeman.csh: man pages can effectively be generated by running
1381 this script. Symbolic links are made from $CCP4/man/cat1/ to the $CDOC
1382 files which are then viewable by `man`.
1383 ** $CINCL/ccp4.setup: $CMAN has been removed and $CHTML = $CCP4/html has been
1384 added. $CCP4_BROWSER added - it is to be the path and name of an html browser
1385 to be used for viewing ccp4 documentation. ccp4help alias added to run
1386 $CCP4_BROWSER with file $CHTML/INDEX.html
1387 * MAKEFILE.COM: "DEC Fortran" is no longer a valid test between Alpha and
1388 VAX. Test has been changed.
1389 * MAKEFILE.MMS: has been removed as it was out of date. Nobody noticed so
1390 perhaps everyone is using the makefile.
1391 * MOSFLMBITS.COM: has been removed because it is no longer needed.
1392 * configure: changed building of shared library for OSF1. Also, `pwd`
1393 changed to `pwd`/ as there may have been problems installing the shared
1394 library. The -with-mosflm option is being removed. The library routines
1395 mdw 1.37 are not need for the new version of MOSFLM. --tmpdir=DIR option added.
1396 g77 is now the default compiler for linux - not fully tested.
1397
1398 * Program changes:
1399 * AGROVATA: program labels changed from I+ to I(+) etc. to be consistent
1400 with SCALA and TRUNCATE.
1401 * BONES2PDB: now recognises BONES_ATOM_XYZ and BONE_ATOM_XYZ as valid
1402 datablock headers, as well as SKEL_ATOM_XYZ.
1403 * CROSSEC: input now fully keyworded.
1404 * * DM: have version 1.8.1 from Kevin. The 'solvent flipping' option has been
1405 removed and solvent flattening and histogram matching are compulsory.
1406 * ECALC: now has an option "SNB" which outputs E's in the format
1407 Shake-and-Bake reads.
1408 * FFT: P222 and P2221 have been removed as valid FFTSPACEGROUPs becuase of
1409 errors in calculating the maps. The C222 (21) routines are now working
1410 properly.
1411 * FFT,FFTBIG: there was a chance that F could be negative if bias removed.
1412 Fixed so that F > 0. ABCOEFFS file altered to avoid mis-interpretation.
1413 * FHSCAL: now has an option "CENT" which uses only centrics for scaling,
1414 which may be more accurate in space groups with a lot of centrics such
1415 as tetragonal
1416 mdw 1.37 * HKLVIEW: changes to handle MNFs. Partials were not added properly, now
1417 fixed.
1418 * MAMA2CCP4: automatic format identification didn't work for VMS. Fixed.
1419 * MLPHARE: format error when using 'PRINT RMSF RMSE' fixed. Problem with
1420 FOM out of range 1.0 - 0.0 fixed. New APPLY keyword for applying
1421 refined scales to derivative data. Maximum number of derivatives
1422 increased to 20. Reflections could have been rejected incorrectly if
1423 data was anomalous but had no deltaF. Now fixed.
1424 * MTZ2VARIOUS: new option INCLUDE FREER to select just freer set.
1425 If FREE column included and not used in INCLUDE/EXCLUDE options, then
1426 OUTPUT TNT will now output it.
1427 * MTZDUMP: new HEADER keyword, with corresponding -e option to mtzdmp.
1428 * * NCSMASK: problem with keyword 'OVER' removed.
1429 * * NPO: fixed one bug with USEORTEP. Probably others. FILE keyword removed
1430 now must assign coordinate input to XYZIN1, XYZIN2 ...
1431 * OVERLAPMAP: END keyword added, error in xloggraph output removed.
1432 * PROTIN: New CONTACTS subkeywords for extended anti-bumping checking.
1433 New SPECIAL SYMM and CHNTYP SPECIAL RESN <> TO <> keywords.
1434 * POSTREF: keyword ABSORPTION replaced with INSCALE
1435 * REBATCH: DETECTOR option added, for use with SCALA. Added BATCH [ALL] option.
1436 * * RESTRAIN: New Version 4.5 added.
1437 mdw 1.37 * ROTAPREP: an extra input option has been added MTZI. Also, new keyword
1438 DETECTOR has been added for use with SCALA. It now also outputs MNFs in
1439 columns which are not appropriate (eg XDET, YDET). CELL keyword will
1440 override the cell read in from DENZO or MTZ formats.
1441 * * ROTAVATA: program labels changed from I+ to I(+) etc. to be consistent
1442 with other programs.
1443 * * SCALA: new version 2.3.1 from PRE. Has made AGROVATA and ROTAVATA
1444 obsolete.
1445 * SCALEPACK2MTZ: output labels changed from I- to I(-) etc. to avoid
1446 problems with parser. Missing data treatment added. New keywords
1447 ANOM and CELL.
1448 * SCALEIT: checks on keyword combinations of ANALYSE, SCALE and REFINE
1449 now applied. Anisotropic scale was not applied when using SCALE. Also, if
1450 SCALE card used then the scales specified are not refined.
1451 * SFALL: checks to see if symmetry assigned (not all options have HKLIN).
1452 * SIGMAA, TRUNCATE, WILSON: typo found in the subroutine LSQ. Effects the
1453 fitting of the straight line through the Wilson PLot.
1454 * SOLOMON: can now read various O mask formats, can decide automatically
1455 which. However, will only output CCP4 masks.
1456 * SORTWATER: corrected syntax of NCS ... SAME command
1457 * SURFACE: FORMAT BNL renamed PDB.
1458 mdw 1.37 * * TRUNCATE: input columns IW(+) etc. now not used (scalepack2mtz doesn't
1459 produce them). Corrections to MNF handling. Input labels now I(-)
1460 instead of I- etc. ANOM OFF now works. It has been changed to use form
1461 factors from atomsf.lib rather than an internal table. This means that
1462 more atom types can be catered for. The values are different from before
1463 so there will be slight differences from earlier version of truncate.
1464
1465 * Library:
1466 * MTZLIB: there was an inconsistency between program labels being case
1467 insensitive and file labels being case sensitive. Now both are case
1468 sensitive. WARNING; program labels must be in upper case when specified
1469 in LABIN.
1470 * RWBROOK: these routines have been changed extensively because of the
1471 proposed change in format for co-ordinate files. This should be
1472 transparent to users (although some programs have been altered, check
1473 documenation) but developers will need to conform to the new routines.
1474 More details can be seen on the Web in the Developers Section.
1475
1476 * New programs:
1477 * ARPP: AUTOMATED REFINEMENT PROGRAM from VICTOR S. LAMZIN.
1478 Note that "arp" has been renamed "arpp" to avoid conflict with unix command.
1479 mdw 1.37 * GETAX from Clemens Vonrhein. Real space searching for rotation axis of
1480 a D<n> or C<n> multimer (<n> = 2,3,4,5,6,...).
1481 * OMIT from Bauke Dijkstra and Fred Vellieux. Calculate omit maps
1482 according to procedure of Bhat.
1483 * RDENT: create dictionary entries for Restrain from PDB file.
1484 * STNET moved from unsupported
1485 * REVISE: program to generate normalised anomlous scattering factor
1486 magnitudes from MAD data (Yao Jia-xing).
1487 * wulff.ps added to 'aggregated' stuff, for generating Wulff
1488 net (Ian Clifton).
1489
1490 * Documentation:
1491 * All program documentation has been converted to html. These are now the
1492 master copies and the plain text docs are generated from them. Man pages are
1493 formally dead. If you set up a cat1 directory pointing to $CDOC then you can
1494 continue to use the man command. A "whatis" file is distributed in
1495 $CHTML so that you can still use man -k or apropos.
1496 * $CCP4/man and $CCP4/unsupported/man have been removed.
1497 All files are now in $CDOC and $CHTML.
1498 * $CHTML/matthews_coef: unforunately the initial formula for Vp was
1499 incorrect and has now been corrected.
1500 mdw 1.37 * Some new flow charts added to manual.
1501
1502 * Examples:
1503 * $CEXAM/unix/runnable/scalepack2mtz.exam added.
1504 * $CEXAM/unix/runnable/agrovata.exam and $CEXAM/unix/runnable/rotavata.exam
1505 removed. If you need an example, you should be using scala.
1506 * $CEXAM/tutorial: the MTZ files which are part of the tutorial are now
1507 distributed as NA4 files. Problem with file names in MR tutorial fixed.
1508 * All *.sh have been converted to *.exam files because of the problems with
1509 viewing these with netscape.
1510
1511 * Withdrawal:
1512 * $CETC/cman: this utility has been withdrawn, as the man pages are now dead.
1513 * $CLIBS/chelp.c and $CLIBS/graflib.f will be moved to the 'mosflm-bits'
1514 directory on the anonymous ftp server. They are not required for the new
1515 version of MOSFLM.
1516 * ABSCALE: moved to unsupported directory.
1517 * AGROVATA: moved to unsupported directory. Function has been taken over
1518 by SCALA.
1519 * PLANES: was unsupported, now withdrawn. Functionality is covered
1520 by GEOMCALC. PLANES hasn't been converted to use new RWBROOK subroutines,
1521 mdw 1.37 but if you want the code to hack, call us at DL.
1522 * POSTREF: moved to unsupported directory.
1523 * PROLSQ: moved to unsupported directory. Use REFMAC.
1524 * ROTAVATA: moved to unsupported directory. Function has been taken over
1525 by SCALA.
1526 * SUPERPOSE: function duplicated in both LSQKAB and POLYPOSE.
1527 * DERIV : was unsupported, functions duplicated in SFALL.
1528
|
1529 acr 1.36 Summary of significant changes to CCP4 at version 3.2
1530 ------------------------------------------------------
1531
1532 * Building etc.:
1533 * $CCP4/x-windows/XCCPJIFFY/Imakefile: compiler options for HPUX sent
1534 by Morten Kjeldgaard.
1535 * $CCP4/x-windows/xdlgjk/Makefile: added install and empty-targets
1536 procedures, in line with $CPROG. Added MAKEFILE.COM
1537 * $CPROG/MAKEFILE.COM: procedure for Solomon was causing a warning but
1538 compilation was not affected. This has been fixed to eliminate warning.
1539 Solomon compiled with case sensitivity.
1540 * Compilation of C code changed due to library.h.
1541 * configure: because of problems with the optimisation the default is
1542 now O1 for OSF1. IRIX6.2 section added. Warning messages have been
1543 surpressed for IRIX5*, HPUX A.09.* and OSF1.
1544
1545 * Program changes:
1546 * AMORE: if the B for an atom is zero or below then it is reset to 20.0. A
1547 message is printed if this is the case.
1548 * BONES2PDB: latest version from KDC on 7/10/96.
1549 * DM: lastest version from KDC on 7/10/96.
1550 acr 1.36 * ECALC: resolution keyword is now acted upon.
1551 * F2MTZ: calls to fatal were incorrect.
1552 * FFT: keyword FILL didn't do anything - fixed. New keyword GRID SAMPLE to
1553 specify the sampling grid as a fraction of the resolution. FFTs in P2 did
1554 not work properly and has been removed. P1 should be used instead of P2.
1555 * FHSCAL: labels DANO and SIGDANO changed to DPH and SIGDPH to be consistant
1556 with SCALEIT.
1557 * IPDISP: spdfils have been changed for MARs. -Ms is now a bigmar with
1558 squashed format. -Mo has been removed but is equivalent to -M. -m small
1559 mar in original format. All these are big endian. -V is the same and
1560 now -v is small mar from VAX i.e. little endian.
1561 * MAMA2CCP4: latest version from KDC on 7/10/96.
1562 * MAPMASK: latest version from KDC on 7/10/96.
1563 * MAPROT: latest version from KDC on 7/10/96.
1564 * MLPHARE: problems with printing MNFs when monitoring reflections fixed.
1565 * MTZ2VARIOUS: typo in defining external function was causing compilation
1566 problems. Now fixed. EXCLUDE FREER will now exclude any freeR subset. Any
1567 FreeR sub-set in the MTZ file can be output as the FreeR set to XPLOR,
1568 SHELX. Dummy columns IDUM?? have been added, these will output as integers
1569 in USER mode. An mmCIF file of the reflection data and associated data
1570 can now be generated. XPLOR output changed to output SIGMA instead of SIGM.
1571 acr 1.36 * MTZDUMP: FORMAT keyword introduced so that the reflection list can be
1572 output in a certain format. Resolution limits are applied to the overall
1573 statistics. Missing reflections are flagged with '?'. Ranges are now calculated
1574 for the partial statistics tables (STATS keyword).
1575 * MTZUTILS: the UNIQUE option data from file 2 was output instead of file 1.
1576 Bug now fixed. Associated columns properly scaled with SCALE option.
1577 * NCSMASK: latest version from KDC on 7/10/96.
1578 * POLYPOSE: Bugs fixed so that default values work if FIX and INCLUDE not
1579 specified.
1580 * POSTREF: the column label 'ABSFAC' and 'SIGABS' have been changed to
1581 'SCALE' and 'SIGSCALE' in order to work with output from SCALA.
1582 * PROCHECK: a write statement in PPLOT was over 132 characters. Changed
1583 the write to avoid this. Only a problem with VMS.
1584 * PROTIN: +PROLSQ & REFMAC the format of the PROTOUT file has changed so
1585 that the files will not be compatible with last version. Change is so that
1586 residue numbers up to 9999 are allowed.
1587 * REFMAC: Output FOM as well. Made P1 default symmetry. Now supports cubic
1588 spacegroups. Defaults have changed since last version please read the
1589 documentation.
1590 * RESTRAIN: updated to version 4.3.5 from Ian Tickle. Isotropic Bs are
1591 written out properly when outputing aniso. Us.
1592 acr 1.36 * ROTAPREP: the way the batches are handled is now more consistant. NBATCH
1593 keyword has been removed, the number of batches is taken from the file
1594 where appropriate. MISBATCH keyword added to specify missing batches.
1595 * SCALEIT: interesting stats. on large isomorphous/anomalous differences
1596 produced for REFINE and ANALYSE modes. Normal probability analysis now
1597 seperates centrics and acentrics. Now outputs Kraut scale instead of
1598 reciprocal.
1599 * SIGMAA: problem with missing FC sorted.
1600 * SOLOMON: CCP4 masks were not being read properly, now fixed. O style
1601 rotation and translation operators do not have to have the header line.
1602 Problems have have been caused when averaging using CCP4 masks, now
1603 resolved.
1604 * TRUNCATE: divide by zero problem fixed. The output now contains H K L
1605 F SD Dano SD F+ SdF+ F- SdF- Imean SD I+ SdI+ I- SdI-. Also, scaling with
1606 the Wilson plot is compulsory.
1607 * XDLMAPMAN and XDLDATAMAN: removed system dependent routines. Altered the
1608 menu and io windows so there are sized flexibly. Also, added command line
1609 qualifier so font for menu can be changed.
1610
1611 * New programs:
1612 * MAKEDICT: will produce TNT or PROTIN dictionary entries from a PDB
1613 acr 1.36 or PROTIN file.
1614 * MATTHEWS_COEF: written by Misha Isupov to calculate the Matthews
1615 coefficient given the cell, symmetry, number of atoms etc..
1616 * RASMOL: RasMol 2.6 (unix and VMS versions) are now distributed with CCP4.
1617 * SCALEPACK2MTZ: Convert SCALEPACK output into an MTZ file. It then must
1618 got through TRUNCATE to convert to Fs.
1619
1620 * Library:
1621 * $CLIBD/(no)chiral_pep*.dic: correction to ARG sidechain.
1622 * $CLIBD/atomsf_neutron.lib: Change atomic number of D to 101 to bring
1623 into line with RBROOK.
1624 * chelp.c: some irregularities fixed.
1625 * chelp.h: machine dependent stuff now in library.h.
1626 * library.c: integer type was incorrectly defined for Big-endian
1627 machines with CONVERT_FROM set.
1628 * library.h: has been created from library.c. This will contain the machine
1629 dependences required for all C programs.
1630 * mtzlib.f: bug in LRREFL fixed; affected BIOMOL programs.
1631 * rwbrook.f: s/r SFREAD moved here from AMORE,MLPHARE,REFMAC,SFALL
1632
1633 * Documentation:
1634 acr 1.36 * RSTATS: document brought in line with prog. FREE keyword added.
1635 * Tutorials: a new set of tutorials have been made in five main areas:
1636 MIR, MR, refinement, density moification and MAD. These procedural scripts
1637 can be found in $CEXAM/tutorial.
1638 * html versions of the documentation for most of the main programs are
1639 in $CCP4/html Point your browser at $CCP4/html/INDEX.html
1640 * x-windows/doc: file names have been changed but essentially the *.txt
1641 files are similar to the old *.doc* files.
1642
1643 * Withdrawal:
1644 * ROTAVATA: will be unsupported in release 3.3. SCALA will become the
1645 recommended program.
1646 * PROLSQ: will be unsupported in release 3.3. REFMAC will become the
1647 recommended program.
1648
|
1649 acr 1.34 Summary of significant changes to CCP4 at version 3.1
1650 ------------------------------------------------------
1651
1652 * Building etc.:
1653 * configure: fftbig, tracer and amore have individual compile
1654 flags for AIX. OSF/1 optimisation reduced to -O1; problem
1655 with FFT SCALE card suggests compiler problem.
1656 * include/environ.def,default.def: refmac files added.
1657 * CPROG:MAKEFILE.COM: typo in linking of refmac corrected.
1658
1659 * Program changes:
1660 * General: A number of programs were found to close files on program
1661 termination. This may cause problems on some machines. Here
1662 is a list of progs. that were changed (not all programs have been
1663 checked): abscale, act, agrovata, almn, contact, coordconv, crossec,
1664 extend, f2mtz, fft, fftbig, gensym, geomcalc, hgen, hklplot, icoefl,
1665 mlphare, mtz2various, mtztona4, npo, pdbset, peakmax, polarrfn, prolsq,
1666 protin, rfcorr, rotaprep, rstats, sortwater, undupl, vectors, volume.
1667 * FFTBIG: compiler/runtime problems caused by undefined LNAN fixed.
1668 * FHSCAL: problem with eof on input corrected. LIST can take a no. > no.
1669 of refls. without crashing. Statistics for old style MTZ the same as
1670 acr 1.34 new.
1671 * FREERFLAG: systematic absences are now not assigned a freeR flag but
1672 are flagged as missing. When using the COMPLETE keyword the freeR flag
1673 information is taken from the MTZ file and not the keyword input.
1674 * HKLVIEW: minv replaced by minv3 because of routine renaming in
1675 modlib.f (see 3.0).
1676 * MAMA2CCP4: problem fixed wrt quotes in call to ccperr.
1677 * MLPHARE: compiler problems caused by undefined CCPNUN fixed.
1678 * MTZ2VARIOUS: keyword NaN replaced by MISS.
1679 * MTZDUMP: missing reflections are printed as "MNF". The VALM keyword
|
1680 acr 1.36 has been removed.
1681 * PROCHECK: now the first atom in *.new is printed only once. CONVAX
1682 has now beenons are printed as "MNF". The VALM keyword
|
1683 acr 1.34 has been removed.
|
1684 acr 1.35 * PROCHECK: now the first atom in *.new is printed only once. CONVAX
1685 has now been added to distribution.
|
1686 acr 1.34 * PROTIN: error in handling of multiple disordered planar groups fixed?
1687 Atoms now must have VDW radii defined. Hence, changes in dictioaries.
1688 * REFMAC: several fixes.
1689 * ROTAPREP: can now convert user-defined format to multi-record MTZ
1690 file (INPU USER).
1691 * SOLOMON: (solomon.c) parameters for rbfro1 were undefined.
1692 * STEREO: keyword CONSTRAIN could not be used, now working.
1693
1694 * Library:
1695 * SYMLIB: maximum no. of symmetry operators increased to 192. Now
1696 consistent with MTZLIB. Error in handling P2 C unique corrected.
1697 * $CLIBD/protin.dic: all atoms have VDW radii defined. Changed OXT and OE
1698 for NFORMYL and NACETYL so they are consistant with OT.
1699 * $CLIBD/protin_jp.dic: extra terminal atoms (OE, OXT) added to terminal
1700 residues similar to protin.dic.
1701 * $CLIBD/protin_vl.dic: extra terminal atoms added to terminal
1702 residues similar to protin.dic.
1703
1704 * Examples:
|
1705 acr 1.35 * *.log-dist: all files except completedata and na4tomtz have been removed
1706 from the $CEXAM/toxd area. Some files have been added to the
1707 $CEXAM/unix/runnable area.
|
1708 acr 1.34 * Solomon.sh: incorrect keyword was changed. Error in reading map files
1709 corrected.
1710 * $CETC/uniqueify: original cell now retained rather than rounded up version.
1711 Problem with some refls. not being assigned a FreeR flag overcome.
1712 -f switch modified to accept <label> argument. -p <fraction> switch added.
1713 * $CETC/UNIQUIFY.COM: added. VMS version of uniqueify
1714
1715 * Documentation:
|
1716 acr 1.35 * hgen: included this time.
1717 * mtzutils: RZONE described correctly now.
1718 * Solomon: MULSOLV keyword incorrectly referenced in the doc as
|
1719 acr 1.34 SLVMUL.
|
1720 acr 1.35 * mtzmnf: clarified that columns not specified in LABIN are output
|
1721 acr 1.34 unchanged.
|
1722 acr 1.35 * unique: improved description of uniqueify script.
|
1723 acr 1.34
|
1724 acr 1.33 Summary of significant changes to CCP4 at version 3.0
|
1725 fx 1.32 ------------------------------------------------------
1726
1727 * Building etc.:
1728 * ccp4/etc/PROCHECK*.COM: hopefully the problem with PRODIR$ is now
1729 sorted.
1730 * XCCPJIFFY: SUNOS_5 added to Imakefile, SUNOS_4 hints in comments.
1731 * Irix6 configuration is provided, your mileage may vary -- it did for me.
1732 Feedback still wanted.
1733
1734 * Program changes:
|
1735 acr 1.33 * AMORE: The HKLM keyword has been reinstated. Default NM=25. Fix: all
1736 0kl reflections of table were 0. Keyword END now accepted. Fix possible
1737 problems with inverse FFT due to dimensioning error. Fix failure to get
1738 FFT prime factors right. Less likely to overflow limits on HKL. SORTFUN
1739 can generate a table -- enables use of Es for TRAFUN. Maximum value for
1740 TRAFUN NMOL <nmol> increased to 9. The ROTATE NSR keyword reinstated.
1741 * CAD: The scale factor is now applied to the correct columns and not to
1742 inappropriate ones like phase.
1743 * DM: correct multi-domain averaging bug. DM 1.6 now current version.
|
1744 fx 1.32 * ECALC: Use LABIN and LABOUT rather than FOBS/ISODIFF -- incompatible
|
1745 acr 1.33 change. Introduced SCALE card to scale F and F2OR.
|
1746 fx 1.32 * F2MTZ: Deal with SHELX free R.
|
1747 acr 1.33 * FFT/FFTBIG: A new keyword has been added FILLIN which substitutes F2 for
1748 F1 if F1 is missing. This only works if the MTZ file has been properly
1749 converted to Missing Number Flags.
1750 * FHSCAL: Resolution card added so that data can be truncated in output
1751 file.
|
1752 fx 1.32 * FREERFLAG: Default semantics of free R column changed, along with its
|
1753 acr 1.33 type: it's picked from a set of integers, allowing full cross-validation.
1754 An existing free R set may be completed when reflections are added (only
1755 if using missing data conventions).
|
1756 fx 1.32 * HKLPLOT: Redimensioning, improved output.
1757 * IPDISP: spdfil.mar_n now image type "bigovf", to indicate overflow
1758 table. ipdisp -m option points to spdfil.mar_n (bigend rather than
1759 littleend image)
1760 * MLPHARE: Phasing power was printed as 0.0 with PRINT AVE. SCALE FP option
1761 removed. Resolution in Angstroms is added to tables but not plotted on
1762 xlog-graphs. SCRIPT keyword will produce either a VMS COM file or unix
1763 script with refined heavy atom parmeters. Ensure Angstrom coordinates are
|
1764 acr 1.33 in PDB format - Orthogonal code 1. Will now produce NaNs for unphased
1765 reflections.
|
1766 fx 1.32 * MTZ2VARIOUS: Remove RESTRAIN input type (never actually necessary
1767 since restrain can specify the input format) now restrain reads MTZ. OUTPUT
1768 USER will now output DP and SIGDP. For USER the ordering of the columns is
|
1769 acr 1.33 taken from the ordering on LABIN not LSPRGI table. If reflection record
1770 has NaN, by default reflection not output. NAN keyword will output them.
1771 * MTZDUMP: Missing data identified through MNFs. File statistics table
1772 now gives single "Mean" and "Mean abs." which is calculated from all
1773 non-missing data in a column. LRES option added to list resolution.
1774 More flexible statistics available via STAT keyword.
|
1775 fx 1.32 * NA4TOMTZ: Fix incorrect call of `qnan'. (Unlikely to have caused problems
1776 before missing data changes.)
1777 * NPO: colours are now consistant with those defined in XCCPJiffy. CHAIN
1778 sub-keyword removed. Input handling improved a little. JOIN RADII HBOND
1779 now works as it should. Msecst has been reinstated. Can now have maps
|
1780 acr 1.33 stacks like 3,5,7 or 5,10,15 etc.. RADII BOND ALL fixed.
|
1781 fx 1.32 * OVERLAPMAP: changed code for EXCLUDE option. Will have non-zero point in
1782 mapout if |grid_point| < 1.0e-06 in map1.
|
1783 acr 1.33 * PDBSET: new keywords added EXCLUDE HEADERS, EXCLUDE HYDROGENS and SEQUENCE
1784 [PDB|SINGLE].
|
1785 fx 1.32 * PHISTATS: output improved + documentation.
1786 * PLTDEV: `-pen' option now works (e.g. for colour PostScript). Colours
1787 are now consistant with those defined in XCCPJiffy.
1788 * PROLSQ: the keyword RTEST has been reconstructed. Now you can only have
1789 RTEST -1|0. This means that you cannot recalculate structure factors i.e.
1790 RTEST +1.
1791 * PROCHECK: Updated to v. 3.3.2 plus fixes.
1792 * PROTIN: Didn't find contacts between the same residue on symmetry related
1793 molecules; error in packed symmtery number caused some contacts not to be
1794 picked up by prolsq; increase some dimensions; error in checking special
|
1795 acr 1.33 inter-chain distances; no longer monitors short hydrogen bonds. Can now
1796 use atom names which represent ions e.g. Fe+2, U+6 etc. Non-protein residue
1797 atoms all assigned as side-chain not as main-chain and side-chain.
1798 * RFCORR: arrays for PARSER redimensioned to avoid problem with TITLE. Polar
1799 angles are output correctly when have exact 2-fold axes.
|
1800 fx 1.32 * ROTAPREP: Format for SCALEPACK options changed from F8.1 to F8.0. Also,
1801 updated man page.
|
1802 acr 1.33 * ROTMAP: the table printed after the OUTPUT ... keyword was incorrect, now
1803 fixed.
|
1804 fx 1.32 * RSPS: Failed to handle SGs with Patterson symmetry groups 143-145.
|
1805 acr 1.33 * RSTATS: OUTPUT ASIN changed to LABOUT ALLIN. PROCESS FOBS should work.
1806 Ranges in F applied to Fobs only. Xloggraph altered and new column added
1807 ln(<Fo>/<Fc>) v resolution.
|
1808 fx 1.32 * SCALEIT: failed for more than 9 derivatives
1809 * SFALL: Reads formfactors automatically if not specified, but still no way
|
1810 acr 1.33 to distinguish Fe Fe+2, Fe+3 except to enter manually. Obsolete keywords
1811 removed.
|
1812 fx 1.32 * SIGMAA: `PARTIAL DAMP' didn't work. HLAC ... HLDC now output correctly.
|
1813 acr 1.33 Map cofficients can now be constructed for missing reflections.
1814 * SORTMTZ: now not only does there need to be an equal number of columns in
1815 each file but the column types must be equal.
1816 * SURFACE: trapped uninitialised variable, important for output.
1817 * TRACER: prog. now works correctly.
|
1818 fx 1.32 * TRUNCATE: MTZ columns were potentially scrambled for data not from
1819 agrovata containing anomalous data.
1820 * ZEROED: initialised some variables to stop IOT trap failure.
|
1821 acr 1.33 * Handling of `missing' data in files added to:
1822 abscale, absurd, agrovata, almn, amore, ecalc, f2mtz, fft, fftbig, fhscal,
1823 freerflag, hklplot, icoefl, mtz2various, mtzdump, mtztona4, mtzutils,
1824 na4tomtz, phistats, polarrfn, postref, rotaprep, reindex, rsearch, rstats,
1825 scala, scaleit, sigmaa, sfall, sortmtz, tffc, truncate, unique, uudupl,
1826 wilson.
|
1827 fx 1.32
1828 * New programs:
1829 * CROSSEC: Interpolate cross sections and compute anomalous scattering
1830 factors (thanks to Don Cromer).
1831 * GEOMCALC: Geomtery calculations on molecule (some overlap with `angles')
1832 * HGEN: Generates hydrogen atoms for a protein coordinate file with standard
1833 geometry.
|
1834 acr 1.33 * MAPROT: Map skewing, interpolating, rotating and averaging program.
1835 * MTZMNF: Attempts to identify missing data in an MTZ file, and replaces
1836 the entry with a Missing Number Flag (e.g. NaN).
1837 * REFMAC: Garib's Maximum Likelihood refinement program. Brand new from York.
|
1838 fx 1.32 * RESTRAIN, TLSANL: `restrain' does constrained anisotropic thermal
1839 parameter refinement using the translation/libration/screw-rotation model.
1840 Its feature list says: refinement with restrained geometry, rigid body,
1841 use of amplitude and phase observations, group anisotropic displacement
1842 parameters, disordered solvent corrections (thanks to Birkbeck group).
1843 `tlsanl' provides TLS analysis. Note restrain's keyword input isn't
1844 in the standard CCP4 form.
|
1845 acr 1.33 * SOLOMON: density modification (phase improvement) by solvent flipping.
|
1846 fx 1.32 * SORTWATER: Replaces `watersort'.
|
1847 acr 1.33 * xdlmapman, xdldataman: have been added thanks to Gerard K.
|
1848 fx 1.32
1849 * Library:
1850 * library.nw removed after too many complaints -- source is now library.c
1851 * lib/data/atomsf.lib has comment section added; some programs which read it
1852 altered as a consequence.
1853 * lib/data/crossec.lib: Data file for `crossec'.
1854 * CCPOPN uses /dev/null and NL: interchangeably
1855 * Fatal errors on diskio files now report the filename in question.
1856 * Packed image routines (for mosflm, ipdisp): New version.
|
1857 acr 1.33 * MODLIB: MINV has been renamed to MINV3. A new routine has been added to
1858 calculate the inverses of nth order matrices MINVN.
|
1859 fx 1.32 * MTZLIB: Facilities for dealing with missing data items. [Null attributes
1860 for relational tuples? -- surely not!] Writing files with this facility
1861 should probably not be done since the programs aren't guaranteed to
1862 swallow the results.
1863 * PARSER: Backslash is now a continuation character like `&' and `-'.
1864 * RESTRAIN dictionaries: chiral_pep4.dic dna.dic nochiral_pep5.dic
1865 chiral_pep5.dic nochiral_pep4.dic
1866 * RWBROOK: Add deuterium to atom list.
1867 * SYMLIB: new routine HKLRANGE.
1868 * symop.lib: correct groups 120, 166, 210, 219, 220, 227, 228. File now
1869 subjected to the overdue check for fulfilling group conditions on the
1870 operators.
1871 * x-windows/XCCPJIFFY/XCCPJiffy: colours changed to be consistant with those
1872 defined in NPO. Also, Xloggraph and xplot84driver pen colours are the same.
|
1873 acr 1.33 * Altered write statements so they do not exceed vms write limit of 132
1874 characters.
|
1875 fx 1.32
1876 * Examples:
|
1877 acr 1.33 * All examples updated, inline with current progs.
1878 * Runnable: crossec.sh, fractional-orthogonal, restrain,
1879 unique-free-R (using new $CETC/uniqueify script)
|
1880 fx 1.32 * Non-runnable: restrain.exam, mlphare-MAD modified
|
1881 acr 1.33 * VMS: tracer.com, surface-volume-calc.com
|
1882 fx 1.32
1883 * Documentation:
1884 * FAQ: the plain text version with searching scripts (ccp4faq) are avialable.
1885 Just type 'ccp4faq'.
|
1886 acr 1.33 * MLPHARE: more information about using MAD data.
|
1887 fx 1.32 * Out-of-date manual-usletter.ps removed -- the current one should print OK
1888 on letter paper anyhow.
|
1889 acr 1.33 * Updates to mtzlib, npo, sfall, sigmaa documentation and the ccp4.1 man
1890 page.
|
1891 fx 1.32
1892 * Withdrawal:
|
1893 acr 1.33 * COMPLETE removed, see unique.doc for replacement procedure.
1894 * FAQ in $CCP4 removed. It will be added to FAQ on the Web.
1895 * ENVELOPE, FLATMAP, RESLICE, PRMAP moved unsupported status.
|
1896 fx 1.32 * LCF2MTZ, EXCHANGE and LCFLIB removed in the hope that everyone's using MTZ
1897 files -- still available from Daresbury if anyone is in need.
1898 * PLUTO removed, should now use NPO.
1899 * WATERSORT was broken, replaced by `sortwater'.
1900
|
1901 fx 1.29 Summary of significant changes to CCP4 at version 2.15
1902 ------------------------------------------------------
1903
1904 * Building etc.:
1905 * configure tries to avoid messing with the `unsupported' directory if it's
1906 not present.
1907 * HPUX: don't set (invalid) amore (non-)optimisation flags. The correct one
1908 reported to be needed, though.
1909 * include/ccp4.setup-dist: Incorrectly (for any system) set _RLD_LIST,
1910 causing chaos with dynamic loading on Irix and similar systems.
1911 * MAKEFILE.COM: can now compile just one designated program with no checks.
|
1912 fx 1.30 * Fix problems building procheck on VMS.
|
1913 fx 1.29
1914 * Program changes:
1915 * CAD: Allow longer LABIN/LABOUT lines. Accept LABIN FILE <i> ALL.
1916 * CONTACT: The output has changed to: Res type, Res ID, Atom name.
|
1917 fx 1.30 * IPDISP: Support MacScience scanner.
|
1918 fx 1.29 * MAPMASK: Symmetry expansion speeded up. New SIGMA option for SCALE
1919 (useful when contouring).
1920 * MTZUTILS: Fix zeroed columns from hklin2 for reflexions not in hklin1 with
1921 UNIQUE option.
1922 * NCSMASK: A crude `sphere mask' can be constructed by making a PDB file
1923 with only a few atoms and specifying a large radius. Output map grid was
1924 always 3A round coordinates -- now 2A+<rad>.
1925 * PEAKMAX: symmetry related peaks at the edge of the map are not output.
1926
1927 * Library:
1928 * QNAN from the diskio routines (almost unused) changed from a function to a
1929 subroutine to avoid lossage with f2c's calling conventions.
1930 * protin.dic: Last block wasn't read. WAT residue changed to contain more
1931 extensive list of waters (oxygen) only. All other atoms (ZN1,CU) have been
1932 removed.
1933 * symop.lib: Errors corrected in SGs 43, 112, 115, 160, 210, 228, 230 (a
1934 subset of errors reported with the X-PLOR version...)
1935
|
1936 fx 1.30 * Examples:
1937 * Remove unnecessary test_brk.brk
1938
|
1939 fx 1.29 * Documentation:
1940 * Several .doc files corresponding to man .1 files were missing. diskio.doc
1941 was out-of-date.
|
1942 fx 1.30 * Various fixes/updates to documents for amore, ccplib, contact,
1943 libsymmetry, lsqkab, ncsmask
1944
1945 * Withdrawl:
1946 The programs scheduled for withdrawl aren't taken out of this realease,
1947 which is mainly to fix bugs.
|
1948 fx 1.29
|
1949 fx 1.26 Summary of significant changes to CCP4 at version 2.14
1950 ------------------------------------------------------
1951
1952 * Building:
1953 * XCCPJIFFY: Fix problems on Convex (but see comments in Imakefile).
1954 * x-windows/README: The note about patches for xdl_view was obsolete.
1955 * HPUX: Get the right version of the date routine under HPUX9. Attempt to
1956 cope with `Convex' variant (gosh).
1957 * Linux (and other) compilation with f2c: now assumes use of the `fort77'
1958 script (untested on Linux so far)
1959
1960 * Program changes:
1961 * AMORE: tidy up keyworded input: some dubious input which previously worked
1962 may now be rejected.
|
1963 fx 1.27 * CAD: errors in keywords are now trapped better.
|
1964 fx 1.26 * DERIV: fixed bug in atom input
1965 * DM: multitudinous ways to enter averaging matrices; skeletonisation
1966 facility; output solvent masks could be ragbled in some SGs
1967 * ECALC: More tables and xloggraph markup.
|
1968 fx 1.27 * FFT: grid sampling for P31(144) is now Nx=Ny=6n Nz=6n, for P21212a(1018)
1969 Ny=4n Nz=2n and for P61(169) Nx=Ny=6n Nz=12n.
|
1970 fx 1.26 * HKLVIEW: reciprocal lattice spacing value in the output area was always
1971 zero during a "measure"; rationalization of maximum resolution handling;
1972 -rawname option.
1973 * MAMA2CCP4: Allow Uppsala compressed format (re. O FAQ Q.731).
1974 * MTZUTILS: Error is produced when two output columns are the same when
1975 using INCL/EXCL. Problem with potentially using random resolution limits
1976 fixed. Now defaults to ONEFILE if HKLIN2 not assigned and also checks for
|
1977 fx 1.27 HKLIN; per old documentation but wasn't implemented previously. UNIQUE
1978 option failed when there were more reflections in hklin2 than in hklin1.
|
1979 fx 1.26 * NPO: RESIDUE EXCL now works as it should. Plus documenation more in
|
1980 fx 1.27 line with program. DCELL now works and map axes labels are always plotted.
1981 Open scratch file in the scratch area.
|
1982 fx 1.26 * PDBSET: new options SYMGEN NCS, SELECT OCCUPANCY; fixed bugs in RENUMBER
|
1983 fx 1.27 input and in reading O datablock; new options BFACTOR MAXIMUM|RANGE,
1984 SELECT BFACTOR, COM, REPLACE ATOM. O data blocks can now have comments and
1985 case insensitive to data block type i.e. R
|
1986 fx 1.26 * PEAKMAX: Output overflow is now fixed.
1987 * POLARRFN: ticks at 0, 90, 180, -90 are now sensible.
1988 * PROCHECK: Version 3.3 (less the NMR stuff). See $CPROG/procheck/README
1989 (no new manual). New script procheck_comp for comparing related
1990 structures (also proplot_comp), both untested.
1991 * PROTIN: Deal with multiplanar groups automatically. Re-dimension to cope
1992 with current default dictionary. VDW contact checks weren't being done
1993 between different chains in the same molecule. More consistency of error
1994 messages so they can be found in the output.
1995 * ROTAPREP: With RAXISDUMP (& WEIS) input only: for MPART>1, IPR would have
1996 a garbage value. For SCALEPACK input: initial records shouldn't be read
1997 as reflexions; strong reflexions were being read wrongly, effectively
1998 divided by 10 because of inconsistent formatting by scalepack.
|
1999 fx 1.27 * RSEARCH: Does dynamic memory allocation.
2000 * RWCONTENTS: Don't write to unconnected unit.
|
2001 fx 1.26 * SCALA: wrong values to be output in the modified SD columns SIGIC,
2002 SIGIPRC, iff the input file contained a SCALE column (ie if the output
|
2003 fx 1.27 file from Scala had been run into the input for further scaling); fix
2004 wrong reflection counts and array overflow with FINAL FULL.
|
2005 fx 1.26 * SFALL: The documentation and some output messages have been amended to
2006 clarify confusion about the setting of nonstandard atom/residue types to
2007 ZZZ/DUM. Some messages are now only output with VERBOSE. PG name could
2008 get corrupted, confusing dm. For P4i2i2 SGs, phase was wrong for centric
2009 reflexions h 0 l with h+l divisible by 3. Now checks for reflexions in an
2010 incompatible AU for the SFSG requested. P3-specific SF and refinement
2011 routines added.
|
2012 fx 1.27 * SIGMAA: map coefficients for PARTIAL and COMBINE changed, new labels --
2013 see doc. Two sets of experimental phases can now be merged (with or
2014 without HL). COMBINE syntax changed. Phase analysis transferred to
2015 PHISTATS.
2016 * UNIQUE: DEAFULT keyword for dummy column contents.
|
2017 fx 1.26 * WATPEAK: bad subroutine call could cause crash. Error fixed in calculation
2018 of symmetry equivalents. Error in output fixed. Dmin default is now 0.1
2019 and output expanded.
2020
2021 * Library:
2022 * KEYPARSE: New module providing a higher-level interface for decoding
2023 keyworded input.
2024 * lib/data/protin.dic: Residue flags corrected per protin change. Fix to
2025 avoid fatal error in protin.
2026 * lib/data/protin_jp.idl: Format error for group DFP causing problems even
2027 when the group not used.
|
2028 fx 1.27 * lib/data/symop.lib: typo in 72th symmetry element of F432 (209).
|
2029 fx 1.26 * MTZLIB,SYMLIB: SYMFR{2,3} no longer reset the start column to 0 and check
2030 for a SYMM keyword there.
2031 * PLOTSUBS: correct coordinate transformations used by PLTDBU, PLTMBU
2032 * PARSER: The IDEC value returned by PARSE(R) was rubbish for integers and
2033 not per doc for reals -- definition for integers rationalised (changed).
2034 * RWBROOK: New routine RCELL to return cell parameters; remove the EJD
2035 feature whereby atom types could be stored in columns 67-80 and clash with
2036 footnotes. In RBROOK atom type ' W' is now Tungsten and not water.
|
2037 fx 1.27 * CCPOPN: Fix the Unix special case for /dev/null with CCP4_OPEN=UNKNOWN.
|
2038 fx 1.26
2039 * New Programs:
2040 * BONES2PDB: Convert BONES output to pdb file.
2041 * MAPMASK: General map and mask manipulation program; can replace `extend',
2042 `envelope', `prmap'.
2043 * NCSMASK: Performs operations on non-crystallographic symmetry masks,
2044 e.g. as a precursor to DM.
|
2045 fx 1.27 * PHISTATS: Phase analysis (the ANALYSE part of the old SIGMAA). NB. It is
2046 probably more informative to do map correlation.
|
2047 fx 1.26 * POLYPOSE: A program for superimposing many multi-domained structures.
2048 Written by R. Diamond.
2049 * PROCHECK scripts, programs: procheck_comp, proplot_comp, mplot, rmsdev
2050 (see above).
2051 * STEREO: To reconstruct 3D coordinates from measurements of stereo diagrams
2052 (from Michael Rossmann).
2053
2054 * Examples:
|
2055 fx 1.27 * For new programs: polypose, stereo
2056 * RF-with-Es, toxd-RF-Es: rotation function with Es
2057 * auto-amore, MR-with-amore: automated running of amore for a simple case
|
2058 fx 1.28 (unrealsitic toxd example removed)
|
2059 fx 1.27 * non-runnable/mapcutting: Prepare P1 map to calculate "model" structure
2060 factors for molecular replacement.
2061 * procheck/procheck_comp: there are VMS examples, although they both can be
2062 run interactively.
2063 * watpeak: Using toxd without the waters as the model. Then generating "new"
|
2064 fx 1.26 waters from an fo-fc map. These new waters can be compared with the
2065 refined ones.
2066
2067 * Documentation:
2068 * (Still insufficient) update of the print{ed,able} manual. It's possible
2069 the description of the distribution in the printed one doesn't quite match
2070 what's here.
2071 * An FAQ is available, for what it's worth.
2072
2073 * Notice of withdrawal:
2074 In the next release PLUTO will be withdrawn in favour of NPO and ROTAVATA
|
2075 fx 1.27 will be withdrawn in favour of SCALA. Also possibly/probably for the chop
2076 as the functionality is elsewhere: extend, reslice, prmap, envelope,
2077 flatmap.
|
2078 fx 1.26
|
2079 fx 1.25 Summary of significant changes to CCP4 at version 2.13
2080 ------------------------------------------------------
2081
2082 * Building:
2083 * Configuration/installation was wrong for dynamic shared library
2084 * Building mosflm-stuff failed if not building a shared library
2085
2086 * Library:
2087 * CCPALC: now zeroes the memory chunk -- affects amore, at least
2088 * protin.dic: New values for protein residues to improve bond angles.
2089 Another co-factor has been added.
2090 * protin_jp.doc: Gives an explanation of how JP dictionary was made. The
2091 default dictionary is based on this.
2092 * SunOS: CCPFYP now sets up abort for common floating point exceptions
2093 * symop.lib: added spacegroup 1003 (P2 with dyad along Z)
2094
2095 * Program changes:
2096
2097 * ALMN: Now reads columns from HKLIN2 correctly.
2098 * AMORE: SIGF is now compulsory. Crashes and garbage output due to
2099 uninitialised data avoided.
2100 fx 1.25 * CONTACT: dimension increased.
2101 * FFT{BIG}: Abcoeffs are now written out correctly.
2102 * NPO: LABEL TEXT wasn't working
2103 * TRACER: input now keyworded and input/output is now to standard
2104 input/output rather than files; avoid crashes on some systems due to
2105 unsaved variables
2106 * WATPEAK: (omitted from 2.12 changes note): SYMMETRY is compulsory because
2107 symmetry related waters are removed.
2108
2109 * Examples:
2110 * Added runnable example for tracer
2111 * waterpeaks now consistent with `watpeak' changes
2112
|
2113 fx 1.23 Summary of significant changes to CCP4 at version 2.12
2114 ------------------------------------------------------
2115
2116 * Building:
2117 * F2C compilation: be conservative about ability to unlink scratch files
2118 (not actually done in 2.11)
2119 * VMS: for DEC fortran remove /noopt in library build and use
2120 /assume=(dummy_aliases) for programs to avoid possible problems with known
2121 illegalities
2122 * A dynamic shared version of the library can be built and installed on
2123 Irix[56] and SunOS5 using the --with-shared-lib option to configure
2124
2125 * Library:
2126 * XDL_VIEW: don't grab inappropriate events with popup
2127
2128 * Program changes:
2129 * ABSURD: allow it ro read antique data
2130 * AGROVATA: fix at 2.11 caused problems with anomalous data
|
2131 fx 1.24 * AMORE: avoid singular matrix from peaksearch on degenerate ridges
|
2132 fx 1.23 * FHSCAL: fix calculation of pseudo cell volume for vecref with multiple
2133 derivatives
2134 * MTZUTILS: didn't find HHL reflections correctly
2135 * NPO: SIG and MAX sub-keywords of CONTRS has been added. Can now contour on
2136 sigma levels or as fraction of the maximum (Atsushi Nakagawa). MAP 3D
2137 option is now reinstated. SYMMETRY input got translation wrong
2138 * PEAKMAX: ensure highest symmetry-related peak not rejected
2139 * PROLSQ: NOUPDATE option expurgated from code and example in doc
2140 * PROTIN: dimensions increased
2141 * REINDEX: avoid /0 etc. problems with null orientation block in input
2142 * ROTAPREP: pick up SIGF column if LABIN not used; abend if no reflexions
2143 passed etc.
2144 * WATPEAK: now has dmin cutoff and will check for symmetry related peaks
2145 to accepted waters.
2146
|
2147 fx 1.20 Summary of significant changes to CCP4 at version 2.11
2148 ------------------------------------------------------
2149
2150 * Building:
2151 * (Unix) binsort didn't get compiled/installed
|
2152 fx 1.23 * IRIX64: 6 is recognised by configure with target `irix' (but we have bad
|
2153 fx 1.20 reports about the 6.0 compiler)
2154 * Irix5.2: avoid X installation misfeature (files installed owned by root)
2155 * F2C compilation: be conservative aboutability to unlink scratch files
2156
2157 * Library:
2158 * XDL_VIEW: bug fixes which probably don't affect ccp4 programs
2159 * lib/data/protin.dic RNA residues have been improved + other changes.
|
2160 fx 1.22 * CCPLIB: correct off-by-one in month value from f2c and AIX IDATE (showing
2161 up in the banner); avoid dates sometimes coming out in US order
|
2162 fx 1.20
2163 * Program changes:
2164 * AGROVATA: numerical problem in rejection in some circumstances; use scala
2165 SIGIC, SIGIPRC columns
2166 * COORDCONV: changes for CSD format at v2.3 were bogus
|
2167 fx 1.21 * CONTACT: translational parts of SYMMTERY were ignored; could fail due to
2168 undefined variables
|
2169 fx 1.20 * HKLVIEW, IPDISP: avoid crash in some circumstances
2170 * MTZ2VARIOUS XPlor output for anomalous data is now correct. Also, DP
2171 sigma cutoff has now been removed.
2172 * NPO the LIMIT keyword works and has been reinstalled.
|
2173 fx 1.21 * OVERLAPMAP: now gives total correlation for main chains and side chains
2174 seperately
|
2175 fx 1.20 * ROTAPREP: check BATCH specification properly and make code easier for
2176 adding new input types
|
2177 fx 1.23 * RSTATS: preserve SIGFC and FREE in output with OUTPUT FOFC
|
2178 fx 1.20 * SCALA: problems with optional columns (manifest with Denzo output, at
2179 least) fixed; Omit "too strong" reflections from initial scaling; New
2180 output columns SIGIC[, SIGIPRC], corrected sd(I), sd(IPR)
2181 * SFALL: potential crashes from unsaved variables
|
2182 fx 1.21 * VECTORS: avoid crashes from coding error
|
2183 fx 1.20
2184 * New programs:
2185 * RFCORR: Analyis of correlations between cross- and self-Rotation functions
2186
2187 * Examples:
2188 * Added runnable examples for: agrovata, rotavata, scala, truncate
|
2189 fx 1.21 * Fixed: tffc_procedure, icoefl
|
2190 fx 1.20
|
2191 fx 1.18 Summary of significant changes to CCP4 at version 2.10
2192 ------------------------------------------------------
2193
2194 * Citation: The appropriate reference for citing usage of the suite is now
2195 Collaborative Computational Project, Number 4. 1994. ``The CCP4 Suite:
2196 Programs for Protein Crystallography''. Acta Cryst. D50, 760--763.
2197
2198 * Building:
2199 * IRIX5.2: [introduced un-noted at 2.8] configure attempts to solve problems
2200 with rewinding scratch files a la 5.1
2201 * rsps compilation ignored the setting of `FC' -- wrong for HPUX, at least
2202 * ipdisp should now build and run under VMS
2203 * `iris3000' configuration removed to avoid confusion with R3000-based Iris
2204 systems -- no evidence it ever worked anyhow
2205 * psaver wouldn't compile e.g. on convex
2206 * AIX: wrong `install' program was used
2207 * VMS: fix makefile.coms for xdl_view, hklview, rsps, creation dates compared
2208 * F2C can be used to compile the suite. This may be of interest to those
2209 who'd otherwise need to buy a compiler. It's adequately fast with gcc.
|
2210 fx 1.19 Use configure flag --with-f2c (unless on linux or freebsd).
|
2211 fx 1.18 * Linux and FreeBSD configurations are available (untested) using f2c
2212 * The `binsort' program has been moved from lib/src to src.
2213 * XDL_VIEW library updated to a newer version that doesn't need patches for
2214 OSF; hklview, ipdisp now use it
2215 * Titan: fixes made but untested
2216
2217 * Library:
2218 * CCPLIB: CCPERR now prints the program name so you can easily see what
2219 failed at the tail of the log file; it should also print error messages on
2220 the unix standard error stream; CCPPNM is a new routine to return the
2221 program name. CCPALC etc. can now cope with 12 arrays, including
2222 LOGICAL*1 (deprecated). CCPOPN messages can now be suppressed using -v as
2223 for QOPEN ones and don't cause write errors with long path names.
2224 * MAPLIB: changed format of mean & RMS density print (Uppsala request); this
2225 might break awk-ward things that look for this information in the old
2226 format-- sorry
2227 * MTZLIB: Change dimensions (and parameterise) to allow 192 symops, not 96.
2228 (3 non-protein groups in symop.lib have this many operators.) LWHSTL is a
2229 new simple interface to LWHIST for writing standard history records. The
2230 mtzlib object size is somewhat smaller. Avoid problems with clashes
2231 between program column labels and file labels when the columns aren't
2232 fx 1.18 actually the same. LOOKUP now initialised as -1 compulsory, 1 soft
2233 compulsory (for agrovata/rotavata etc.) and 0 optional. Other programs
2234 have also been affected.
2235 * pack_c.c: add AIX, HPUX calling conventions
2236 * PARSER: various long-standing lossage in PARSE and PARSER corrected,
2237 especially handling of comments and continuations; now works as documented
2238 in ccp4.1 and the manual, I think. Documentation somewhat improved.
2239 * RWATOM: deleted -- Dimaond format no longer supported by any programs
2240 * SYMLIB: Change dimensions a la MTZLIB; EPSLN now general; some changes to
2241 point group name handling in PGNLAU for consistency with Int Tab.; P61/P65
2242 now NZ=12n.
2243 * symop.lib: typo in SG166
2244 * MAPLIB: Change dimensions a la MTZLIB
2245 * scatcoef.lib obsoleted by changes to vecref
2246 * PLOTSUBS: add routines moved out of polarrfn
2247 * lib/data/hist.lib: added for dm
2248 * lib/data/protin.dic: replaced by John Priestle's, based on Engh/Huber
2249 parameters with York cofactors added.
|
2250 fx 1.19 * lib/data/protin_vl.idl: alternative protin dictionary from Victor Lamzin
2251 (see lib/data/protin_vl.doc)
|
2252 fx 1.18 * BINSORT: programs that do sorting now should always abort (ungracefully)
2253 on disc full errors etc. rather than reporting zero records returned from
2254 the sort and continuing.
2255
2256 * Program changes:
2257 * AGROVATA: partials weren't handled correctly for non-mosflm data; avoid
2258 the need for SCALE with 1 batch; fix array bound errors with all batch
2259 nos. 1
2260 * AMORE: TABFUN accepts NOSHIFT or NOTRAN equivalently; fix failure of
2261 TABLING on some systems due to not closing scratch files; error in
2262 calculation of RF standard deviations; errors in treatment of Miller
2263 indices (which could cause spurious failures) corrected but means that
2264 previously-generated HKLPCK and TABLE files need to be regenerated; TRAFUN
2265 failed in polar space group
2266 * AREAIMOL: potential problems due to uninitialised variables; check for
2267 atomic number written at the end of a PDB line for cases of nonstandard
2268 atom naming, like sfall.
2269 * BAVERAGE: changes to output
2270 * CAD: RESOLUTION OVERALL wasn't obeyed
2271 * EXTEND: proper action if symmetry mangled: if SG number <= 1, set to P1,
2272 else bomb with message; make check against asymmetric unit volume a
2273 fx 1.18 warning, so that it can work in projection
2274 * FFT: Grid in P61/P65 must now be NZ=12n.
2275 * FHSCAL: can scale up to 20 datasets; BIAS now defaults to 0 (assuming the
2276 worst of the data processing program).
2277 * FREERFLAG, MLPHARE, REINDEX, SFALL, SIGMAA: add history to HKLOUT
2278 * HKLVIEW: draws labelled axes
2279 * IPDISP: correct calculated resolution of outer circle. Async I/O removed
2280 to work on OpenVMS. Dialogue box no longer locks screen.
2281 * MAPSIG: keyworded; could loop on default input due to uninitialised
2282 variable
2283 * MLPHARE: Parameters reset properly HLA .. HLD and FHn, FHAn are now
2284 correct on output. LABOUT ALLIN works + program checks to see if input
2285 column labels are the same as program labels.
2286 * MTZ2VARIOUS: TNT output option and EXCLUDE FREER option; USER output
2287 option; SHELX output flagged for free R if appropriate
2288 * MTZDUMP: include zero values of type H, P or A in the resolution
2289 statistics
2290 * NPO: LABEL FIX atom_name and LABEL atom_name now work properly. LABEL
2291 atom_name was not accually possible before. Also input cards echoed in
2292 output.
2293 * OVERLAPMAP: PATTERSON option (a la GROPAT)
2294 fx 1.18 * PDBSET: REORTHOGONALIZE and REPLACE RESIDUE options
2295 * PEAKMAX: symmetry-related peaks not output
2296 * PLTDEV: fixes to scaling for PostScript output
2297 * PRMAP: end-of-file on input now just prints map header
2298 * PROCHECK: version 3.0.1 as released by Roman Laskowski, but with some
2299 programming errors fixed and using CCP4 file opening routines. Includes
2300 colour plots etc. New manual in $CDOC/procheck.doc and
2301 $CCP4/manual/procheck/manual.ps. Note the accompanying licence in
2302 $CPROG/procheck/confid.doc
2303 * PROTIN: default dictionary improved (see above)
2304 * ROTAPREP: reading XDS files and F+, F-, sigmas are now root(2)*SIGIMEAN.
2305 * ROTAVATA: didn't accept MAXWIDTH keyword to pass to agrovata; fail
2306 gracefully when zero reflexions accepted in a batch
2307 * ROTMAT: wouldn't run without complaining about missing CRYSTAL; slight
2308 additions to output
2309 * RWCONTENTS: count of hydrogens was wrong
2310 * SCALA: Made phi range errors warnings up to maximum of 50 errors; SKIP
2311 option; OUTPUT OMIT PARTIALS option: Don't keep partials if not being used
2312 for scaling (should speed things up)
|
2313 fx 1.19 * SCALEIT: now defaults to NOWT option (ignore SDs of data); new keyword
2314 WEIGHT to use SDs.
|
2315 fx 1.18 * SFALL: Improve some error messages; SFSG now defaults to an appropriate
2316 value (highest symmetry consistent with the data) so you don't have to
2317 look one up. Grid in P61/P65 now NZ=12n. LABOUT ALLIN works + program
2318 checks if input column labels are the same as program labels. Using
2319 FPART PHIPART was broken.
2320 * SIGMAA: new option to set resolution limits for phase combination
2321 ("COMBINE LOW|RESOLUTION")
2322 * TFFC: allow much longer buffer for entering input label assignments which
2323 may be needed in some cases
2324 * VECREF: new keywords RCUT, DAMP; use atomsf.lib scattering factors rather
2325 than scatcoef.lib; improved treatment of large Bs; sites with low
2326 occupancy or silly B factors not output; allow negative occupancies; THRE
2327 & BLIM options; dynamic memory allocation.
2328 * WILSON: END keyword; coding error caused failure sometimes
2329
2330 * New programs:
2331 * DM: all-singing, all-dancing density modification: solvent flattening in
2332 one program, histogram mapping, Sayre's equation, molecular replacement...
2333 See also the document doc/dm_ncs_averaging.doc
2334 * MAMA2CCP4: convert Uppsala-format masks from MAMA to CCP4 format (`mapman'
2335 isn't currently correct on this)
2336 fx 1.18 * RESLICE: A simple-minded resectioning program; interchanges axes in core
2337 ("unsupported")
2338 * STNET: Generate stereographic net plot for use with polarrfn
2339 ("unsupported")
2340
2341 * General:
2342 * History records written to HKLOUT now mostly have date and time included
2343 to give a better chance of figuring out sequences if necessary.
2344 * Keyworded input may give less unpleasant surprises now due to fixing of
2345 `parser'
2346 * Vestiges of Diamond format coordinate files removed
2347
2348 * Examples:
2349 * Original toxd dataset had wrong column type for ANAU20
2350 * examples/vms is now much fuller
2351 * Updated or added examples in examples/unix/runnable: mir_steps, vecref.sh,
2352 scaleit.sh, patterson (replaces fft.sh), dm.sh, 3fofcmap, f2mtz.sh &
2353 mtz2various.sh (using free R and X-PLOR type), rsps.sh, fhscal.sh,
2354 polarrfn.sh, scaleit.sh, mtzutils.sh, npo.sh
2355
2356 * Manual:
2357 fx 1.18 * Minor changes to the text -- no new printed version currently.
2358 * To format the LaTeX for US letter paper (rather than A4) uncomment
2359 `\letterpapertrue' at the top of manual.tex and run `dvips' appropriately.
2360 The result is now available as manual-usletter.ps.
2361
2362 Summary of significant changes to CCP4 at version 2.9
2363 -----------------------------------------------------
2364
2365 * VMS: reading MTZ files basically didn't work from v2.7 -- records were
2366 essentially all zeroed under most circumstances
2367
2368 Summary of significant changes to CCP4 at version 2.8
2369 -----------------------------------------------------
2370
2371 * Building:
2372 * PSAVER wouldn't build under DEC Fortran (broken at 2.7, sigh)
2373 * VMSDISKIO compiled with some fortran versions, despite containing junk,
2374 but not with others
2375
2376 * Library:
2377 * PARSER: avoid problems with @-included files which, e.g. caused `unknown
2378 fx 1.18 keyword' problems with @-files of solutions read back into amore
2379 * SYMOP.LIB: 2 typpos: `_' for `-'
2380
2381 * Program changes:
2382 * MLPHARE: Bug for MAD data: it assumed it could estimate the centric phase
2383 from the the first FH, which doesn't work if your first FH = 0.0.
2384 * SFALL: UnSAVEd variables could cause failure sometimes
2385
2386 Summary of significant changes to Csignificant changes to CCP4 at version 2.7
|
2387 fx 1.14 -----------------------------------------------------
2388
2389 * Building:
2390 * HPUX: Enable some floating point traps in OS v9 and remove abort on all
2391 other signals
2392 * The `ranlib' step was omitted after the mosflm-stuff target in the
2393 library; affects BSD-like unixes
2394 * VMS: The MAKEFILE.COMs would only work with DEC Fortran (OpenVMS) (?)
2395 through using a .F extension
2396
2397 * Library:
2398 * IRIX 5.1: enable rewinding of scratch files (at the expense of them not
2399 being deleted if the program crashes); there may be other problems with
2400 irix5.1
2401 * IPDISP: changes for building in VMS (yet untested)
|
2402 fx 1.17 * MAPLIB: MSYCPY mangled the symmetry information if maps were transported
2403 between machines with different byte orders; affects programs extend,
2404 overlapmap, mapreplace, zeroed
|
2405 fx 1.14 * MTZLIB: speed up reading and writing MTZ files somewhat by avoiding a
2406 subroutine call for each datum
2407 * VMSDISKIO: efficiency improvements and QINQ now works (but never used?)
|
2408 fx 1.15 * XDL_VIEW: typo prevented compilation; Makefile altered; (untested) VMS
2409 MAKEFILE.COM
|
2410 fx 1.14
2411 * Program changes:
2412 * AGROVATA: removed VAXtran; BINS RECIPROCAL option allows binning by equal
2413 volumes in reciprocal space
2414 * BAVERAGE: code polished
|
2415 fx 1.16 * COORDCONV: fix possible uninitialised variable; maybe speed up reading of
2416 X-PLOR format
|
2417 fx 1.14 * FFT{BIG}: coding error caused core dumps in some cases
2418 * MLPHARE: increase maximum refinement cycles
2419 * MTZUTILS: resolution restriction didn't always work with two files
2420 * PEAKMAX: The incorrect peak height (NEXT peak in the sorted list rather
2421 than current) was being written to the output Brookhaven file in the
2422 "occupancy" column.
2423 * PROLSQ: VDW contacts not used properly; fixes to allow variable
2424 non-crystallographic symmetry
2425 * PROTIN: fixes to allow variable non-crystallographic symmetry; increase
2426 maximum number of atoms
2427 * ROTAVATA: BINS RECIPROCAL allowed in line with agrovata
2428 * ROTMAT: insist on CRYSTAL input
2429 * SCALA: bugs affecting INTENSITIES PARTIALS option
2430 * SFALL: source code re-vamped; error with ALLIN and >29 columns; problem
2431 with error estimate could cause failure; removed SAVEs to give
2432 optimisation a better chance.
2433 * SIGMMA: phase analysis instrumented for xloggraph
2434 * VECTORS: allow atom lines to have extra fields on end
2435 * WATPEAK: two new totals; dimensions increased
2436
2437 * Documentation changes:
2438 fx 1.14 * FFT: correct some SG-dependent info
2439 * FHSCAL, VECREF: minor changes
2440 * ROTMAT: more explanation/clarification
2441
2442
2443 Summary of significant changes to CCP4 at version 2.6
2444 -----------------------------------------------------
2445 * Building:
2446 * SYMLIB: non-standard fortran
2447 * OSF/1: unaligned access wasn't fixed
2448
2449
|
2450 fx 1.13 Summary of significant changes to CCP4 at version 2.5
2451 -----------------------------------------------------
2452
2453 * Building:
2454 * Typpos caused failure on: ESV (/Titan?), VMS
2455 * OSF/1: `make' infelicity caused failure; OSF check missing from chelp
2456 (mosflm bits only); OSF `fsplit' failed on rwbrook.f, symlib.f; mtzlib
|
2457 fx 1.14 caused unaligned access errors on OSF/1 (generally wrong for 8-byte C
|
2458 fx 1.13 longs)
2459 The xdl_view-based code won't work asis (due to 64-bit pointers).
2460 `x-windows/osf-patches' supplies patches specific to OSF/1 pending a new
2461 version of xdl_view.
2462 * AIX: amore optimisation flag wrong
2463 * VMS MAKEFILE.COMs now try to reset working directory sensibly
2464 * SCALA directory needed re-naming for make to work
2465 * MSTAMP omitted from makefile
2466 * RSPS sometimes printed symmetry operators wrong
2467 * ccp4.setup-dist had a typo in the XUSERFILESEARCHPATH definition
2468
2469 * Library:
2470 * Dynamic memory allocation was wrong for integer arrays -- they only got
2471 half as much as they should have done. Might have affected amore results.
2472 * CCPLIB: add CCPNUN for finding unconnected i/o unit.
|
2473 fx 1.14 * QSEEK errors now hint that the file may be corrupt.
|
2474 fx 1.13 * PARSER: avoid echoing lines when reading `@'-file e.g. symmetry headers
2475 from agrovata
2476 * SYMLIB: SYMTRN was wrong for operators n/4
2477
2478 * Program changes:
2479 * AMORE: improve error messages
2480 * HKLVIEW: can display columns other than of type F or J (eg W)
2481 * IPDISP: minor changes and new detector types
|
2482 fx 1.14 * MLPHARE: minor corrections - aniso eigen vectors not printed
|
2483 fx 1.13 * PLTDEV: fix picture range selection
2484 * SCALA: cope properly (?) with absent orientation blocks; if scaling with
2485 fullys only, skip reflections with le. 1 full (this speeds things up a lot
2486 in many cases); doc change
2487 * SFALL: didn't cope with an MTZ file with RESO 0
2488 * XCCPJIFFY: changes for OSF/1 had been omitted
2489
2490
|
2491 fx 1.11 Summary of significant changes to CCP4 at version 2.4
2492 -----------------------------------------------------
2493
2494 * Building:
2495 * library.c wouldn't compile with Sun bundled compiler and probably other
2496 K&R ones
2497 * amore optimisation flag was invalid on Sun with SunPro compiler (at least)
2498 * rsps compilation flags changed for Irix to try to avoid v. long
2499 compilation and reported compiler crashes
2500
2501 * Library:
2502 * SYMLIB: PG 321 was written out with the `PG' missing
2503 * PARSER: bug with lines exactly 133 characters long
2504
2505 * Program changes:
2506 * AGROVATA: fix in absence of MPART column
2507 * AMORE: rotfun could output garbage; dimension was set incorrectly for
2508 sorting step
2509 * BAVERAGE: error in xloggraph output
2510 * DISTANG: change error report
|
2511 fx 1.12 * ECALC: coding error with PG name
2512 * FFT: wasn't removing scratch file (at least in VMS)
|
2513 fx 1.11 * GENSYM: can now generate more than one cell
2514 * MLPHARE: can now use 20 derivatives
2515 * MTZ2VARIOUS: read Is ready for SHELX
2516 * NPO: bugs in GRID command
2517 * PDBSET: add ELEMENT option; typo could cause bad error message
|
2518 fx 1.12 * POLARRFN: small error in calculation of mean & rms
|
2519 fx 1.11 * RSPS: attempt to remove illegal code had broken the command loop --
2520 current version may not compile (correctly)
2521 * ROTAPREP: fix batch number for XDSUNIQUE, TEXHKL, MUI, MUF; generalise (?)
2522 DENZO
2523 * RSTATS: error for PROCESS FOBC (width multiplied by scale factor for every
2524 reflection)
2525 * SCALA: flow.h and refflg.h were missing; make XDET, YDET, ROT columns
2526 optional if not used
2527 * SCALEIT: can now use 20 derivatives
|
2528 fx 1.12 * TFFC: coding error with PG name
|
2529 fx 1.11
2530
|
2531 fx 1.10 Summary of significant changes to CCP4 at version 2.3
2532 -----------------------------------------------------
2533
2534 * Administrivia: CCP4 is now funded by the Biotechnology and Biological
2535 Sciences Research Council following the demise of SERC. Note also the new
2536 FAX number for CCP4 if you need it.
2537
2538 * Change policy to avoid the distinction between major and minor released
2539 versions: too much work and scope for mistakes.
2540
2541 * Most Fortran files now .f rather than .for as required ages ago by the
2542 Working Group: more convenient on un*x and no problem on VMS.
2543
2544 * VMS library: C code replaced by (faster) VMS-specific Fortran
2545 (vmsdiskio.for), avoiding an apparently insurmountable RTL library bug. The
2546 script MOSFLMBITS.COM an be used to build the extra library modules for
2547 MOSFLM if required.
2548
2549 * Free R factor facilities: programs affected (only additions): freerflag,
2550 sfall, fft, mtz2various, f2mtz, rstats. Note the opposite convention to
2551 X-PLOR -- free R flag is a weight (but not yet used as such). The
2552 fx 1.10 conventional way to arrange calculation of the free R from an mtz file is by
2553 using `LABIN FREE=FreeR_flag'. See individual program documentation and
2554 some altered examples.
2555
2556 * Manual and examples: various fairly minor updates.
2557
2558 * Library:
2559 * changes on termination: try to give helpful system error message and not a
2560 misleading one, fix problems with EXIT on AIX, HP-UX and ISATTY on AIX;
2561 * Some scratch files weren't being deleted under Irix. They should now
2562 vanish, possibly unless the program crashes.
2563 * [ccplib] CCPALC, CCPALE, CCPE2I: facility for dynamic memory allocation
2564 (mainly for amore so far); correct handling of `-d' command-line flag.
2565 * [diskio] MSYWRT: added; properly-typed variants of QREAD/QWRITE: QREADR
2566 etc.;
2567 * [modlib] RANMAR, RMARIN: random number routines added
2568 * `magic number' code for absent data flags was completely bogus, fortunately
2569 not used;
2570 * add CCPMVR, CCPZR, CCPCPI;
2571 * SYMLIB: avoid possibly echoing symop file due to undefined variable;
2572 changes in step with symop.lib PG changes; remove 80-character limit on
2573 fx 1.10 SYMMETRY input.
2574 * PLOT84LIB: tidying up and removal of undefined variables
2575 * Fix problems with read/write diskio files on SunOS, ESV, Titan, at least.
2576
2577 * lib/data/symop.lib now has all standard SGs (and some non-standard) and
2578 correct PG names; symop_all.lib removed.
2579 * lib/data/protin.dic: format error in the planar restraints of the NACETYL
2580 group
2581 * lib/data/VLdict.dic was bogus -- removed. The default protin dictionary
2582 is what this was supposed to be.
2583
2584 * Installation:
2585 * Titan may now work;
2586 * VMS .com files changed, especially for `make'-like facility in
2587 CPROG:MAKEFILE.COM to avoid re-building up-to-date programs; now don't
2588 need a C compiler for the basic library (as above);
2589
2590 * New programs:
2591 * REBATCH: alter batch numbers in an unmerged MTZ file (saves running Mosflm
2592 again); beware -- not well tested.
2593 * FREERFLAG: tags each reflection in an MTZ file with a flag;
2594 fx 1.10 * MSTAMP: add machine stamp to MTZ or map files lacking it (unsupported);
2595 * PSAVER: partial symmetry averaging;
2596 * SCALA: scale together multiple observations of reflections (rotavata
2597 replacement, previously aggregated);
2598 * SYMFIT: fit best molecular transformations to sets of coordinates related
2599 by non-crystallographic symmetry (unsupported).
2600 * X-WINDOWS THINGS: the XLOGGRAPH, XPLOT84DRIVER, IPDISP and HKLVIEW
2601 programs are now considered part of CCP4 (previously aggregated). The
2602 sources live in $CCP4/x-windows. They aren't built and installed with the
2603 rest of the programs. Modify the makefiles in the individual directories.
2604
2605 * Withdrawn:
2606 * HEAVY: use mlphare;
2607 * POLSIG: unnecessary with current polarrfn.
2608
2609 * Program changes:
2610 * ACT: wouldn't run in many cases;
2611 * AMORE: dynamic memory allocation -- can change dimensions without
2612 recompilation (but doesn't necessarily reduce the virtual memory needed);
2613 small fixes; some Spanish translation!
2614 * AGROVATA: Re-dimensioning. FSAFE option now works. Added WIDTH WILSON &
2615 fx 1.10 WIDTH SQUARE options for alternative binning on intensities. Change
2616 binning of partial bias correction analysis to allow bias of +-20% rather
2617 than +-10%. Significant changes to allow addition of partials spanning
2618 more than 2 images, and to make use of the new column MPART containing the
2619 partiality indicator output by MOSFLM. These changes are essential to
2620 deal with data from MOSFLM version 5.20 or later versions. New keyword
2621 MAXWIDTH specifies maximum allowed width (in images) for partials.
2622 * BAVERAGE: correct format error
2623 * CAD: default resolution to agree with documentation; got lattice type wrong
2624 * COORDCONV: changes for SHELX and Cambridge database input; code tidied
2625 * ENVELOPE, FLATMAP: Avoid use of logical*1 true/false in mode0 map -- can't
2626 transport results between compilers.
2627 * EXTEND: remove check on input map starting at grid point 0,0,0, also fixed
2628 minor bug (which caused some unnecessary work in a few cases). Assumed
2629 (incorrectly) that all asymmetric units were mapped from point (0,0,0).
2630 * F2MTZ: `X' column type for X-PLOR free R fudge; correct format error in
2631 example.
2632 * FHSCAL: END keyword, runnable example.
2633 * FFT{BIG}: defaults for Patterson SG were broken. SG47 was not actually
2634 wrong if not defaulted, contrary to previous alarm. fftbig now does
2635 dynamic memory allocation. HKLMAX option for anisotropic resolution
2636 fx 1.10 (strongly discouraged for normal use). Allow explicit symmetry operators
2637 without bombing. Allow sensible input of multiple scales [Bfactors] from
2638 the same line. Logic error for phase of reflexions with |Fph(calc)|=0 in
2639 double difference maps.
2640 * GENSYM: now writes out CRYST1 & SCALE lines to PDB file; new READ option;
2641 ATOM lines can have extra fields.
2642 * LSQKAB: dimensions increased
2643 * MLPHARE: output tidied; redimensioning; all reflections written out even
2644 if not phased; correct labels for 5th, 6th derivatives
2645 * MTZ2VARIOUS: Free R flag added and o/p compatible with X-PLOR. For any
2646 phase columns present must negate the phase when generating the Friedel
2647 pair. This applies to solvent correction term and PHIB term. Option to
2648 read columns DP, SIGDP, ISYM for anomalous differences, to write out hkl &
2649 -h-k-l if Danom present. Avoid mangling indices sometimes. Didn't reject
2650 reflections with SIG=0.0. EXCLUDE, FPMAX, FPHMAX, FSQUARED, SCALE
2651 options. RESTRAIN o/p type.
2652 * MTZTONA4/NA4TOMTZ: run-length encoding option; NaNs in the file handled
2653 properly (for use with absent data when implemented elsewhere).
2654 * MTZUTILS: SCALE option.
2655 * NPO: avoid calling GETENV (bogus in VMS); fix for different contour
2656 colours at some level
2657 fx 1.10 * OVERLAPMAP: ADD option
2658 * PDBSET: UTOB option
2659 * PLTDEV: not outputs conforming PostScript; default scaling still broken.
2660 * POLARRFN: correct logical name COEFFS; NOPRINT option
2661 * PROCHECK: coding corrections. Un-mangled procheck.doc. Note that there
2662 is a newer version available from
2663 ftp@bsmcha1.biochem.ucl.ac.uk:pub/procheck for which we don't have
2664 distribution permission and which isn't for commercial use. v3.0.1 has
2665 coding problems with undefined/unsaved variables for which you can get a
2666 patch from us if these cause problems.
2667 * PROTIN: check VDW contacts in first chain when only one chain present.;
2668 re-dimensioned; default NCODE = 1 (only matters if you input CELL here);
2669 check array bounds and report all errors in input at the end.
2670 * ROTAPREP: reorganise code to make additions easier; update documentation,
2671 especially lies about formats; fix bad batch numbers with DENZO input;
2672 BATCH compulsory; SCALEPACK input only wrote the first I which broke
2673 rotavata with INTENSITIES PROFILE
2674 * ROTAVATA: avoid array bound errors and undefined variables.
2675 * ROTMAT: corrections, particularly for Merlot NCODE.
2676 * RSPS: updated version from Stefan Knight;
2677 * RSTATS: partial re-write and add free R.; END keyword; avoid infinite loop
2678 fx 1.10 due to numerical problems
2679 * SFALL: disallow both RMSSHIFT and STEPSIZE; free R factor; use NOSCAL if
2680 map input; other alterations, especially for ARP use.
2681 * TFFC: SPACEGROUP/SYMMETRY now optional.
2682 * WATPEAK: would only read first chain; write coordinates of each peak to LP
2683 output
2684
2685
2686
2687 Summary of significant changes to CCP4 at version 2.2.4
2688 -------------------------------------------------------
2689
2690 * abscale: over-long format
2691 * act: wouldn't run in many cases
2692 * agrovata: avoid integer overflow
2693 * cad: default resolution agrees with doc
2694 * gensym: wasn't built by unix Makefiles
2695 * mlphare: long-standing error in figure of merit table
2696 * prolsq: wasn't listing bad distances
2697 * rotaprep: wrong for TEXHKL; initialise some variables (e.g. gave bad batch
2698 with denzo)
2699 fx 1.10 * rotavata: assumed static allocation
2700 * rsps: bad format writing score table
2701 * sfall: problem if SMIN = 0.0
2702 * watpeak: would only read first chain
2703 * examples/toxd/solflat-cyc: add NOSCALE in sfall
2704 * lib/data/protin.dic: format error
2705 * mtzlib: error in Groningen changes in LRREFF possibly causing
2706 reference of unset variable; LWBTIT incorrect: affects rotaprep
2707 output, in particular
2708 * build on AXP VMS: problems with com files, C code; allow for vax number
2709 format
2710 * vms library: prints process time at end, not session
2711
2712 Summary of significant changes to CCP4 at version 2.2.3
2713 -------------------------------------------------------
2714
2715 * scaleit: problems with xloggraph o/p
2716 * almn: bad rms density calculation
2717 * deriv: didn't open hklin
2718 * mtzvarious: correct X-plor o/p
2719 * library:
2720 fx 1.10 * problems with rewinding some scratch files on Convex, ESV; setting logical
2721 NATIVEMTZ ignores file machine stamp in reported VMS case where files had
2722 bad stamp
2723 * problems with CCP4_OPEN hadn't been properly corretced at 2.1.1, sigh
2724 * ESV: avoid configure lossage if /usr/ucb isn't on path (shouldn't it be?)
2725 * examples: correct peakmax o/p in a couple of cases
2726 * proclean: uninitialised variables corrected (probably doesn't matter)
2727 * exchange: wouldn't write the LCF file (the only place it's allowed)
2728 * mosflm bits (image packing) wouldn;t build on osf/1
2729
2730 Summary of significant changes to CCP4 at version 2.2.2
2731 -------------------------------------------------------
2732
2733 * binsort building still failed (some unix only)
2734
2735 Summary of significant changes to CCP4 at version 2.2.1
2736 -------------------------------------------------------
2737
2738 * configuration/building: error building rsps (unix) and procheck (VMS) and
2739 binsort (some unixes). Other changes for Concentrix only.
2740 * polarrfn: plotting error
2741 fx 1.10 * prolsq: check for BATOM set but not XYZB in sfall
2742 * protin: long standing error affecting intra-chain special distances
2743 * Library errors causing general problems:
2744 * setting CCP4_OPEN other than to UNKNOWN was treated wrongly in some cases
2745 * maplib: serious array bound error
2746 * parser: failure to read E-format real numbers
2747 * lib/data/symop_all.lib: corrected
2748 * examples/unix/runnable/waterpeaks: previously omitted
2749
2750 [Note that polsig is actually obsoleted by changes to polarrfn.]
|
2751 ccp4 1.1
|
2752 fx 1.3 Summary of significant changes to CCP4 at version 2.2
2753 -----------------------------------------------------
|
2754 ccp4 1.1
|
2755 fx 1.4 * Binary file transparency: the low-level i/o routines can now read MTZ and
2756 map files written on architectures with different number formats *providing
2757 they are written with this version of the library*. There is some overhead
2758 in this, but no significant overhead reading files written on the same
2759 architecture.
|
2760 fx 1.2
|
2761 fx 1.4 Note that not all the possible combinations have been tested...
|
2762 fx 1.2
|
2763 fx 1.8 * Categorisation of programs: There is a new `unsupported' category of
2764 programs. (This does not imply that we guarantee support for the others.)
2765 They are supplied asis and we will not necessarily fix them (but still
2766 welcome bug reports or your fixes). Many obsolete programs have been thrown
2767 out completely. You can install only the major programs and not the
2768 unsupported category if you want. There is a new directory: `unsupported'.
|
2769 fx 1.3
|
2770 fx 1.4 * Documentation
2771 * There is a much-expanded, but still incomplete new manual. This includes
2772 material formerly in the `overview' man `page'.
2773 * new directory man/man3 for library man pages (incomplete)
2774 * There is now a document for every program (we hope) and many have been
2775 much revised and improved. Complete formatted copies are supplied, along
2776 with man `whatis' files and the .doc files can be used with the unix man
2777 system. Most of the documents have been examined and revised.
|
2778 fx 1.2
|
2779 fx 1.4 * Examples: the examples/unix/runnable directory has scripts which will run
2780 with the small dataset from examples/toxd (which also contains working
2781 scripts). The `ctest' directory has been removed.
|
2782 fx 1.8
2783 * VMS library support: the VMS assembler routines have been dropped -- we now
2784 only provide the C version of the low-level library routines since we can't
2785 maintain the assembly code.
2786
2787 *You need a C compiler for the VMS compilation now.* See the manual for how
2788 to get the free GCC compiler if necessary (although this hasn't been tried
2789 for building the suite).
2790
2791 The C routines are slower than the old assembler ones -- sorry. If this
2792 proves to be a particular problem, let us know.
|
2793 fx 1.3
2794 * Changes/fixes to configure and makefiles and VMS installation; the latter is
|
2795 fx 1.4 now simpler and cleaner but is not guaranteed in OpenVMS yet -- please let
2796 us know.
|
2797 fx 1.2
2798 * Library bug fixes
2799 * mtzlib: IPRINT=4 didn't print symmetry any more; user label input and
2800 output variables reset in lropen and lwopen
|
2801 fx 1.3 * some timing routines were wrong
|
2802 fx 1.4 * the setting of CCP4_OPEN is now obeyed for MTZ and map files
|
2803 fx 1.7 * BINSORT alignment problem on some architectures
|
2804 fx 1.9 * possible inability to redefine logical names in VMS
|
2805 fx 1.2
2806 * General library updates
2807 * MODLIB: routines removed: match, ma21ad, mc10ad
|
2808 fx 1.5 * MTZLIB: more batches allowed; interpret absence flags from the Groningen
2809 BIOMOL system (just set to zero at present)
|
2810 fx 1.2 * SYMLIB: routines removed: turnip, turn3, decsym, syminv, iminv,
2811 symat; added: patsgp; changes to symop.lib; more batches allowed; new
2812 library data file symop_all.lib has all Int. Tab. A SGs
2813 * FFTLIB: added routines factrz, fndsmp, setlim, setgrd
|
2814 fx 1.4 * GRAFLIB: no longer included by default. routines now in PLOTSUBS removed
|
2815 fx 1.2 * PLOTSUBS: replaced with routines removed from graflib
2816 * removed modules: graphics, hlplib, mdflib, optfftlib, plot9x, lib_kraulis,
2817 frodo_maplib, mthlib, hdrlib
2818 * LCFLIB now won't *write* LCF files
|
2819 fx 1.3 * `ccperr' now tries to report the last system error and times in VMS
|
2820 fx 1.4 * PARSER: new routines RDRESL, GTTREA, GTTINT; the (mis)feature of allowing
2821 arithmetic between values read by the parser has been removed
2822 * MAPLIB: improved precision of RMS & mean calculation
|
2823 fx 1.2 * $CINCL/{default,environ}.def: tidying and commenting
|
2824 fx 1.6 * protin.dic: updated and an alternative provided (VLdict.idl) from
2825 Victor Lamzin
|
2826 fx 1.4 * code for binary file transparency (as above)
|
2827 fx 1.2 * Lots of internal reorganisation
2828
2829 * Significant program bug fixes
|
2830 fx 1.4 * ABSURD: problems with `reindex'
2831 * AGROVATA: xloggraph o/p wrong; default INTENSITIES is PROFILE; changes if
2832 SCALE column present
2833 * ALMN: divide-by-0 errors
2834 * FFT: error for spacegroups P65 (and 61 ..); get Patterson SGs correct
2835 * FHSCAL: several corrections
2836 * HKLPLOT: spurious 'Disagreement between symmetry operators'; error in
|
2837 fx 1.2 multiplicity
|
2838 fx 1.4 * MLPHARE: fix divide-by-zero etc.
2839 * MTZ2VARIOUS: don't output excluded reflexions, treat formats as similarly
2840 as possible; output |FPH-FP| if FPH assigned; END not compulsory; output
2841 always to HKLOUT
2842 * OVERLAPMAP: fix problems of rounding errors in calc. of correlation coeff.
2843 * POLARRFN: failed to calculate rms value; put weighted RMS & mean
2844 into map header; correct sampling intervals in map header
2845 * PROLSQ: can no longer attempt to access hkl{in,out} (lcf files)
2846 * REINDEX: new version
2847 * ROTAPREP: takes DENZO input and madnes for050 files
2848 * ROTAVATA: confusion about FTWO/NOFTWO rejections between ROTAVATA and
2849 AGROVATA; change default on number of batches
2850 * SFALL: various small changes
2851 * VECREF: made consistent with FHSCAL (errors in them cancelled out)
2852 * WILSON: xloggraph plot
|
2853 fx 1.2
2854 * Significant program updates
|
2855 fx 1.4 * ABSCALE: new REINDEX option; changes for mosflm summed partials
|
2856 fx 1.2 * ABSURD: storage increase
|
2857 fx 1.4 * AGROVATA: accepts SCALE column etc.; redimensioned; ROGUES file extended;
|
2858 fx 1.6 changes for mosflm summed partials; negative values of SDADD
|
2859 fx 1.4 * ALMN: peak search changed, restored weighting of RMS & mean
2860 * CAD: fairly major re-write
2861 * COMPLETE: changes for triclinic data etc.
2862 * COORDCONV: was coord_conv
2863 * ECALC
2864 * EXTEND: new algorithm; MAPSYMMETRY option
2865 * F2MTZ: CTYP obligatory; FORMAT option
2866 * FFT, FFTBIG: EXCLUDE option; changes to default grid
2867 * LCF2MTZ: grok multi-record lcf files
|
2868 fx 1.6 * MLPHARE: various
|
2869 fx 1.4 * MTZDUMP: now as previous `dumpreso'
2870 * MTZUTILS: wasn't applying resolution cutoffs to output file
2871 * OVERLAPMAP: CHAIN option; change residue packing
|
2872 fx 1.2 * PDBSET: various extra options
2873 * PEAKMAX: keyworded and various other changes
|
2874 fx 1.4 * PROLSQ: new LIMIT keyword; various other changes
2875 * ROTAVATA: default INTENSITIES is PROFILE; changes for mosflm summed
2876 partials
2877 * SFALL: various changes
2878 * SURFACE
2879 * TRUNCATE: changes to interpolation etc.
|
2880 fx 1.6 * WATPEAK: includes contact list; carries through occupancy, B-factor info.
|
2881 fx 1.2
2882 [Changes to things in the `unsupported' directory not given here, although
2883 many have had some changes.]
2884
2885 * New programs
|
2886 fx 1.4 * ACT: analyse coordinates.
|
2887 fx 1.6 * AMORE: monolithic molecular replacement program.
|
2888 fx 1.2 * GENSYM: symmetry-related sites from atoms and list of vectors within
2889 defined volume
2890 * NPO: new version of PLUTO
2891 * PROCHECK system: stereochemistry checking
|
2892 fx 1.6 * RSPS: Patterson searching (previously aggregated)
|
2893 fx 1.2 * UNDUPL: essential for some data from Madnes (following Absurd).
2894 * VOLUME: polyhedral volume around selected atoms
2895
|
2896 fx 1.4 * Programs deleted or moved to the aggregated directories (with some
2897 suggestions for alternatives):
|
2898 fx 1.2
|
2899 fx 1.4 accsa, area [use areaimol], atconv, atomsf, atpeak [use watpeak], bavsc2,
|
2900 fx 1.6 brk2dia, brkmat, brksort [use procheck], burgess, cadpro, chelp, chkplt,
|
2901 fx 1.4 cli_help, convrnxp, coordswap, crossec, dabs, deg, diffop, dumpreso [use
2902 mtzdump], hlbgen, hlptree, limits [use pdbset or extend], mapbrick [frodo],
2903 mapcont [frodo], mapform [use mapexchange], minlim [use extend/pdbset],
2904 nadia [use angles/procheck], o2brk [O distribution (replaced by pdbset)],
2905 oscgen [with mosflm], patvec [use vectors], pdbrot [with ribbon], pltout
2906 [with ribbon], postplot [with ribbon], peaksearch [use peakmax], resection,
2907 reslicer, ribbon [aggregated], ribrot [with ribbon], rwbred, skewbrk, splitd
2908 [ribbon], symgen [use pdbset], tidytext, transz1, xplor2pdb [use pdbset],
2909 xyzlim, xyz_modify [use coordconv]
|
2910 fx 1.2
2911 * Housekeeping: (All?) the distributed files have been examined and only
2912 relevant ones should now be distributed. All the programs should now print
2913 version (date) information when they run.
|
2914 fx 1.5
2915 * Binaries will normally not be supplied on VMS tapes now. (We can't make AXP
2916 binaries anyway.)
|
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