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Revision: 1.200.2.15, Mon Sep 28 08:19:30 2009 UTC (11 months, 1 week ago) by nds65 Branch: series-6_1 Changes since 1.200.2.14: +3 -0 lines new sfcheck, molrep, ctruncate |
-*- mode: indented-text; fill-column: 78;-*-
Summary of significant changes to CCP4 at version 6.1.3 ("No name")
---------------------------------------------------------------------------
* Building etc.:
* gnu compiler 4.4 compliant
* supports Snow Leopard
* Program changes:
* IPMOSFLM: updated to 7.0.5
* MOLREP: updated to 10.2.33
* SFCHECK: updated to 7.3.14
* CTRUNCATE: updated to 1.0.05
* Graphical User Interface:
* IMOSFLM: updated to 1.03
* Bugs fixed:
* Known issues:
* 3488: IMOSFLM: cannot launch batch jobs from interface
* 3630: SCALEPACK2MTZ: does not read symmetry from input file
* 3894: DBhandles not python 3.0 compliant
Summary of significant changes to CCP4 at version 6.1.2 ("Ingleborough")
---------------------------------------------------------------------------
* Building etc.:
* ccp4.setup-dist renamed ccp4.setup-csh
* ccp4i, crank, imosflm launchers copied to bin directory during
installation
* csh no longer used during installation, all steps use sh
* Program changes:
* POINTLESS: updated to 1.3.9
* SCALA: updated to 3.3.15
* REFMAC5: updated to 5.5.0098. PHOUT added for building of MR solutions
with BUCCANEER
* MOLREP: updated to 10.2.31
* SFCHECK: updated to 7.3.13
* SIGMAA: new version from Ian Tickle
* OASIS: minor update
* Graphical User Interface:
* CRUNCH2: new interface for experimental phasing program
* CRANK: update to 1.3
* database back end off by default
* Bugs fixed:
* 3596: IMOSFLM: requires project directory to exist, fails otherwise
* 3689: POINTLESS loop variable overflow
* 3690: REFMAC5 interface not backwardly compatible
* 3713: REFMAC5 interface amplitude based twin refinement
* 3722: CTRUNCATE in import scaled task
* 3790: MOLREP multi-copy search failure
* 3797: all_load shared library builds under newer linux ld
* 3816: TLSANL anisotropic Us
* various uninitialised variables caught
* Known issues:
* 3488: IMOSFLM: cannot launch batch jobs from interface
* 3630: SCALEPACK2MTZ: does not read symmetry from input file
* 3894: DBhandles not python 3.0 compliant
Summary of significant changes to CCP4 at version 6.1.1 ("The New Inn")
---------------------------------------------------------------------------
* Building etc.:
* intel 11: mostly supported
* Program changes:
* PDB_EXTRACT: updated to 3.004
* REFMAC5: updated to 5.5.0072
* POINTLESS: updated to 1.3.1
* MOLREP: updated to 10.2.23
* SFCHECK: updated to 7.3.10
* CHAINSAW: accepts fasta alignment files
* Library changes:
* MMDB: update to 1.19
* monomer dictionaries: various updates, including CYS-MPR
* Updated interfaces:
* REFMAC5: better integration of SAD refinement
* BP3: interface added
* TRUNCATE: CTRUNCATE options added
* DTREK2MTZ: CTRUNCATE now the default for intensity to SF conversion
* SCALEPACK2MTZ: CTRUNCATE now the default for intensity to SF conversion
* Bugs fixed:
* 3628: ccp4i import task
* 3592: SFTOOLS interface
* 3619: REFMAC5 interface ignoring external file
* 3655: CHAINSAW not deleting CISPEP records from PDB
* 3656: PISA writing to $CCP4/share/pisa directory
* 3558: CAD segv
* Known issues:
* 3488: IMOSFLM: cannot launch batch jobs from interface
* 3596: IMOSFLM: requires project directory to exist, fails otherwise
* 3630: SCALEPACK2MTZ: does not read symmetry from input file
Summary of significant changes to CCP4 at version 6.1 ("Holy Trinity Church")
---------------------------------------------------------------------------
* Building etc.:
* Refmac5.4+ requires a Fortran90 compiler, as do Molrep 10 and Sfcheck
7.3+. Configure tests for this, and disables refmac, molrep and sfcheck
builds if not found (e.g. if compiler is g77).
* ccp4.setup: the environment variable GFORTRAN_UNBUFFERED_ALL is
explicitly set to "Y" in the distributed setup files, to ensure that
the log file output from gfortran-compiled programs is written in
the correct sequence. This may incur a performance penalty however.
* POINTLESS, RAPPER, PISA optionally configured and built with core.
* Program changes:
* AREAIMOL: uses a new "spiral distribution" to divide up the surfaces
of the expanded Van der Waals atoms, which gives significant
improvements to the accuracy and stability of the accessible surface
area calculations - see the program documentation (Ian Tickle).
* CAVENV: program now uses symmetry mates of input molecule unless
SYMM OFF set. Gives protein and solvent volumes within map limits.
* CRANK: updated to version 1.2.0. Greatly enhanced (Raj Pannu)
* IMOSFLM: update imosflm to 1.0.0
* LOGGRAPH: is now able to give a basic view of the XMGR-style
normplot and correlplot output from SCALA, for systems where xmgr(ace)
is unavailable.
* MOLREP: updated to version 10.2.12.
* MOSFLM: updated to version 7.0.4.
* OASIS: updated to OASIS-2006.
* PDBCUR: new option to delete ANISOU records.
* PDB_EXTRACT: updated to version 3.0 (since August 2007)
* PDBSET: estimated molecular weight based on the sequence of residues
is automatically calculated when the SEQUENCE keyword is specified.
* PHASER: updated to 2.1.4. This version covers MR, SAD and combined MR and SAD.
* REFMAC5: updated to version 5.5.0066. This adds twinned and anomalous
refinement (Garib Murshudov, Raj Pannu, Pavol Skubak).
* SCALA: updated to version 3.3.9
* SFCHECK: updated to version 7.3.7.
* Library changes:
* Addition of a new "Diffraction Image" library which also comes with 4 small
jiffies installed in bin - diffdump, printpeaks, automask and diff2jpeg.
* Monomer dictionary updated to 4.13
* New programs:
* AFRO: multivariate substructure factor amplitude estimation for SAD/MAD
(Raj Pannu)
* BAUBLES/SMARTIE: new program for re-rendering CCP4 log files with
HTML markup (Peter Briggs & Kevin Cowtan).
* BALBES: automated molecular replacement (Fei Long, Garib Murshudov,
Alexei Vagin).
* cBUCCANEER: statistical model building, optimised for experimental
phasing. (Kevin Cowtan)
* CRUNCH2: direct mothod experimental phasing as part of CRANK (Jan
Abrahams)
* CTRUNCATE: New program for Intensity to Structure Factor conversion and
checking data quality (Norman Stein).
* DBCCP4I: new database server for CCP4i, which includes a graphical
viewer for CCP4i projects plus other tools. (Wanjuan Yang & Peter Briggs)
* IMOSFLM: imported imosflm 1.0.0
* MrBUMP: Automated molecular replacement, search model retrieval and
search model preparation for molecular replacement.
* MTZ2CIF: new program for generating mmCIF reflection files suitable
for deposition, intended to replace OUTPUT CIF option of MTZ2VARIOUS.
See program documentation for more information. (Peter Briggs)
* PARROT: automatic density modification and phase improvement (Kevin Cowtan)
* PISA: the standalone version of the Protein Interfaces, Surfaces and
Assemblies server. (Eugene Krissinel) -- optional
* POINTLESS: Laue and Patterson group determination, v1.2.23. (Phil Evans)
-- optional
* R500: new program for correcting REMARK 500 lines in PDB files.
* RAPPER: conformer modelling through sampling residue rotameric states.
(Nicholas Furnham, Paul de Bakker, Mark DePristo, Reshma Shetty,
Swanand Gore and Tom Blundell) -- optional
* cSEQUINS: Statistical protein chain tracing (Kevin Cowtan)
* SEQWT: new utility to estimate protein molecular weight from the
sequence. (Eleanor Dodson)
* SYMCONV: new utility program for interrogating the CCP4 symmetry
libraries. (Peter Briggs)
* XIA2: Automated data reduction system designed to work from raw
diffraction data and a little metadata, and produce usefully reduced
data in a form suitable for immediately starting phasing and structure
solution.
* Graphical User Interface:
* Version 2.0
* Modules can now include "subfolders" of tasks to help with grouping
related tasks together within a module. These can also be included in
task packages that are exported - however developers should note that
packages created with subfolders are NOT backwardly compatible with
older versions of CCP4i.
* A right-mouse click on the job list presents a "context menu" offering
job manipulation options for the current selection (for example,
rerun or delete jobs). Double-clicking with the left-mouse on a
specific job automatically tries to "rerun" that job.
* Options for customising the colours of jobs displayed in the job list
can be accessed via the "System Administration" and the context menu
described above.
* Viewing files from job in some cases (e.g. Refmac5) now also provides
options (when possible) to launch "plugin" applications (e.g. Coot,
CCP4mg) preloaded with the appropriate data.
* New option to re-import tasks that have already been installed in a
previous version of CCP4 (e.g. Arp/Warp): accessed via the
"Install/Uninstall Tasks" interface in the "System Administration"
menu. (Note that this function requires the user to have permissions
to write files to the CCP4i area.)
* ccp4ish can be run with a "-import_packages <old_ccp4>" option, which
attempts to automatically copy any tasks previously installed in the
CCP4 installation in <old_ccp4>, and add them to the current CCP4i
installation.
* Disabled ("greyed out") tasks can be enabled by setting the appropriate
option in the "Configure Interface" window
* MOSFLM-in-batch: now recognises keywords SYNCHROTRON POLARISATION,
DISPERSION and DIVERGENCE (used for data collected at a synchrotron)
and POSTREFinement keywords WIDTH, MOSADD and MOSSMOOTH.
* PARROT: new interface for the PARROT program.
* PISA webservice: the EBI Protein Interfaces Surfaces and Assemblies
webservice can be launched from the "Structure Analysis" and "Program
List" modules
* POINTLESS: new interface to the POINTLESS program (NB this supersedes
the prerelease interfaces: "Determine Laue Group", "Test Alternative
Indexing" and "Check Centre of Symmetry" - these interfaces can still
be accessed e.g. for reviewing old jobs, but are now deprecated).
* "SFs for Deposition" task (mtz2cif) now uses MTZ2CIF program rather
than MTZ2VARIOUS.
* GetMtzColumnResolution: new command that fetches the maximum and
minimum resolution limits for a specific column in an MTZ file.
* CURRENT_PROJECT and MG_CURRENT_PROJECT parameters are now stored in
status.def (previously in directories.def).
* XIA2: new interface to the XIA2 automated data processing package.
* Annotated HTML logfiles are generated after each program run using
the "baubles" program.
* Made a new task for job colourisation so it is more visible outside
the big configure task.
* Added Dyndom and Chooch interfaces files and added the tasks into
Program list.
* Added the MrBUMP (automated molecular replacement) interface.
* Added new Map & Mask Utilities task to calculate an omit map using
Sfcheck.
* Clipper Utilities: this module has been removed and the Clipper-based
tasks have been moved to other modules, mainly "Reflection Data
Utilities" and "Map & Mask Utilities".
* Added new interface for the existing getax program.
* New task interfaces added to "Data Reduction" module ("Check Data
Quality" folder): "Analysis with ctruncate" and "Analysis with sfcheck"
allow experimental data to be characterised more easily.
* New task interface added to "Molecular Replacement" module ("Analysis"
folder): "Self RF with molrep" provides interface to the self-rotation
function calculation of Molrep.
* autoSHARP: new interface to SHARP/autoSHARP. Needs a separate install
of SHARP/autoSHARP. (Clemens Vonrhein)
* Documentation:
* AREAIMOL: added figures to clarify the definitions of the different
surface types.
* MrBUMP: documentation for MrBUMP, automated molecular replacement
program.
* Withdrawal:
* The following programs have been placed in deprecated/src for future
removal: BEAST (replaced by Phaser), ROTAPREP (replaced by Combat),
ARP_WATERS (use latest ARP/wARP), BPLOT, POLYPOSE, RSEARCH,
RESTRAIN.
* The following X-windows programs have been taken out of the build
procedure, prior to future removal: XLOGGRAPH (replaced by loggraph),
XDLMAPMAN, XDLDATAMAN, IPDISP (replaced by idiffdisp)
* Examples:
* phaser_EP.exam: new example for Phaser 2.1.4, using a sulfur-SAD
dataset for bovine cubic insulin.
* pointless.exam: new examples for pointless
* rampage.exam: new example for rampage mode of rapper
* refmac_sad: new example for refmac SAD target function
* acorn: new example running from 1 Zn atom (Deuterolysin)
Summary of significant changes to CCP4 at version 6.0
-----------------------------------------------------------
* Building etc.:
* Clipper/fftw built by default
* cctbx/phaser are included as separate packages. The main
CCP4 build will build them if these packages are included.
* There are a number of fixes for the AIX build.
* to_small_refmac.csh/to_big_refmac.csh: shell scripts to
reduce and restore the array sizes for Refmac5 prior to
compilation (in $CPROG/refmac5_/)
* A new ccp4.setup-zsh for ZSH users (Bill Scott)
* --with-x is now the default; use --disable-x if you have
problems with the X-windows build
* The script "patch_ccp4.sh" in $CETC can be used to
automatically download and apply available source code fixes
to the suite for UNIX-based systems. Note that any
recompilation must still be performed manually afterwards -
see Appendix M of the CCP4 installation instructions.
* Program changes:
* ANISOANL: now checks for non-positive-definite Us in XYZIN
and lists to log file (all options)
* AREAIMOL: new REPORT keyword allows control of output for
contact areas and reporting of area by residue
* CIF2MTZ: several new column labels added, including anomalous
* COORD_FORMAT: new keyword FIXBLANK
* DM: program now produces a data harvesting file
* MapSlicer: supports reading and display of mask files (new
"mask" mode); displays "greyscale" view superimposed on
contours; saves user preferences for contour levels and other
settings between sessions.
* MTZ2VARIOUS: if F(+) and F(-) are input for SHELX output then
rescaling is done within the program to produce
pseudo-intensities; OUTPUT CIF option updated to use tokens
from the PDB exchange dictionary for anomalous data and HL
coefficients.
* PDBCUR: new keywords SUMMARISE, DELHYDROGEN, MOSTPROB, CUTOCC,
and TRANSLATE (MDW)
* PDB_EXTRACT: new version 2.0
* PDBSET: new function ATRENUMBER (renumber atoms sequentially
without gaps in output file)
* PEAKMAX: new keyword EXCLUDE (turns suppression of peaks at the
edge of the map on or off)
* REFMAC: new version 5.2.0019
* MOLREP: new version 9.0.09
* MOSFLM: new version 6.2.5
* SFCHECK: new version 7.0.18
* SFTOOLS: new options LIST/SET DCELL/DWAVE for dataset information
* Matthews_coeff: outputs the Kantardjieff and Rupp resolution based
probabilities
* FFTBIG replaces FFT
* SCALEPACK2MTZ SYMM keyword not compulsory anymore, will try to pick up
spacegroup in the input file.
* TLSANL: ANISOU line in XYZOUT is now adjusted according to ISOOUT
keyword. Summary tags used to highlight important quantities.
* Library changes:
* CCPERR/ccperror: each time ccperror is called it invokes a
user-defined callback function which has previously been set
using new C library function "ccp4SetCallback".
* CCTBX library included as a separate package (Paul Adams,
Ralf Grosse-Kunstleve et al)
* New programs:
* BP3: multivariate likelihood substructure refinement and phasing
of S/MIR(AS) and/or S/MAD (Raj Pannu)
* CHAINSAW: new molecular replacement utility that mutates a pdb
file to poly-serine using a sequence alignment (Norman Stein)
* PDB_MERGE: jiffy to merge two PDB files (Martyn Winn)
* PHASER 1.3: molecular replacement (Randy Read et al)
* PIRATE (cpirate): statistical phase improvement (Kevin Cowtan)
* SUPERPOSE: secondary structure alignment (Eugene Krissinel)
* Graphical User Interface:
* Version 1.4.4.1
* AREAIMOL: new option to generate pairwise area differences for
"molecules" (defined as arbitrary groups of chains) in a PDB file.
* CRANK: interface to automated structure solution via experimental
phasing (currently SAD, SIR and SIRAS data)
* SHELX C/D/E: interface to running the SHELX C, D and E programs
standalone or as a pipeline in order to perform heavy atom
search and phasing
* CHAINSAW: interface to new program of the same name; mutates a pdb
file to poly-serine using a sequence alignment for molecular
replacement
* PISA webservice: the EBI Protein Interfaces Surfaces and Assemblies
webservice can be launched from the "Structure Analysis" and "Program
List" modules (added in 6.0.2)
* Scale and Merge Intensities (SCALA): option to output Scalepack
formatted reflection files suitable for input into SHELX or SOLVE
(corresponds to OUTPUT POLISH UNMERGED option of SCALA)
* Run Remote Jobs: option to use either rsh or ssh to run jobs on
remote machines.
* Output in different map formats: the interface should now only
offer output in the formats (O, QUANTA) that can actually be
created with the user's setup
* CreateLabinLine4: extended version of CreateLabinLine that allows
groups of up to four related labels to be specified, for example
H-L coefficients or F(+)/sigF(+) and F(-)/sigF(-) groups. This
command also supports a -command option similar to other
CreateLine-type commands. See the documentation for details.
* FindExecutable: new command, return full path of a program
executable
* Install Task: export task now allows save/restore of parameters;
tasks can be defined as basename/directory pairs; version number
included in archive filename.
* Logfile viewer: when viewing a long file, there is now the
option to look at the previous frame as well as the next one.
* MTZ handling: new commands GroupMtzCols, MtzColSameDataset,
GetMtzColType, GetMtzGroupByType.
* WarningMessage: has new options -image, -font and -color
* Superpose: when fitting atoms from one PDB file to another, atom
numbers given by the user now refer to those specified in the file
(rather than to the positions in the file)
* types.def: added new types "_res_file" (ShelxD result file) and
"_phs_file" (XtalView phases file)
* File Selection for Windows: drive can also be chosen from the file
browser.
* Disabled tasks: some task interfaces will be unavailable to users
if "prerequisites" (as defined in the taskname_prereq procedure in the
task interface file) are not found on the user's system.
"Disabled" means that the task button will be non-functional and the
text will be greyed-out.
Check the documentation $CCP4I_HELP/general/additional.html for
information on how to enable these tasks.
* Project Switching: Having a small menu button enabling to instantly
switch between projects without passing through "directories" interface
* Database search/sort: Having a new Button search/sort popping up a window
enabling users to do various kinds of simple/advanced search and/or sorting
also be able to refine sorts or searches.
* CreateToggleFrame: new option -justify allows programmer to specify the
positioning of the subframes (left, right or center).
* Documentation:
* Added documentation on adding doc comments for CCP4i core commands
($CCP4I_HELP/progdocs/documenting.html)
* alternate_origins.html: updated with spacegroup numbers, information
about alternative settings and Hermann-Mauguin symbols
* Loggraphs: documentation for TABLE, GRAPHS, SCATTER etc now in
loggraphformat.html (see "File Formats" section)
* Withdrawal:
* fft (replaced by fftbig )
* Examples:
* abs, bp3, chainsaw, pdb_merge, phaser, pirate, superpose examples added
* New examples for using python interface to cctbx and phaser
(cctbx_py_test.exam and phaser_py_test.exam)
Summary of significant changes to CCP4 at version 5.0
-----------------------------------------------------
* Building etc.:
* configure: convex, stardent, titan, concentrix, ultrix and esv systems
all removed.
* Intel compilers: support for Intel compilers under Linux has been
implemented; use "configure linux_intel_compilers [options]"
* Intel compilers: support for Intel compilers under Linux on IA64
machines has been implemented (by SGI Japan); use "configure
ia64_linux_intel [options]"
* gnu compilers: IA64 support implemented; use "configure linux [options]"
(warning 3.0 broken)
* FreeBSD build: now can use g77 (thanks to Tim Gruene)
* LAPACK/BLAS: CCP4 configuration for NetLib BLAS and LAPACK now includes
all available functions (single, double, complex and double complex)
* Program changes:
* ACORN: updated version: 1) faster translation function using FFT (TRAN).
2) Phase errors can be calculated if true phases are input (LABIN).
* AMORE: substantially updated version: 1) Now estimates memory allocation
automatically (manual assignment is still available). 2) TABFUN: new
keyword BTARGET to adjust model B factors; NORMALISE keyword to generate
normalised model sf's. 3) CLMN: extended number of Bessel functions used
to generate spherical harmonics. 4) Fixes to Locked Rotation Function.
5) TRAFUN: can work with non-crystallographic translation.
* ASTEXVIEWER: please note updated conditions of use (see AstexViewer
documentation).
* BEAST: an MPI version has been added, see $CPROG/beast_/beast_MPI
* CAD: new keywords DRENAME, XNAME and DPNAME. SCALE keyword updated
to accept anisotropic B values.
* CIF2MTZ: new keyword NAME
* COMBAT: 1) new keyword NAME, 2) new option INPUT XDSASCII for reading
file XDS_ASCII.HKL from CORRECT stage of XDS
* COORDCONV: new option INPUT SNB reads SnB peaks files.
* DISTANG: changed format of symmetry/translational operators in logfile.
Note that the OUTPUT DISTOUT option must now be used to generate
output appropriate for input to WATERTIDY.
* DTREK2MTZ: new keywords NAME, WAVE (specifies wavelength of dataset).
* DTREK2SCALA: new keyword NAME
* F2MTZ: new keyword NAME
* FSEARCH: an MPI version has been added, see $CPROG/fsearch_mpi.f
* LSQKAB: increased array sizes (NATOM to 40000, NRS to 13999).
* MLPHARE: significant changes including:
1. ISOE/ANOE now taken (correctly) from last REFINEMENT cycle
2. Checks if two input sites are too close (prevents failures after
RANTAN/SHELX/ACORN if peak search puts a site close to its symmtery
related neighbour)
3. Checks if anom refinement is requested but all AOCC are zero; if
OCC is non-zero when only anomalous diffs are used.
* MAPSLICER/CCP4MAPWISH: 1) Default view changed to be "right-handed",
with option to chnage to "left-handed" view; 2) In "Harker" mode
axes are labelled "UVW" rather than "XYZ"; 3) new option to generate
contours starting from mean density in the map.
* MOLREP: new version 7.5.01.
* MOSFLM: new version 6.2.5
* OASIS: new version 1.2.2.
* POLARRFN: new version extended to order 100 in sph. harm. expansion (from
Ian Tickle). This allows larger integration radius without loss of
resolution.
* PROFESSS: updated version outputs PDB file with the final atoms
* RASMOL: version 2.7.2.1.
* REBATCH: new BATCH XNAME keyword
* REFMAC: version 5.2.
* ROTAMER: updated version has for each Phe and Tyr rotamer Chi(1),Chi(2)
a symmetric one Chi(1),-Chi(2).
* RWCONTENTS: now uses residues from the monomer library: note that numbers
of hydrogens associated with CYS is now 4 (was 5), with HEM is 30 (was
17). Also, calculates I000 (square of atomic formfactors) from input
coordinates.
* SCALA: version 3.2.14
* SCALEPACK2MTZ: new keyword NAME
* SFALL: new keyword NAME
* SFCHECK: version 6.0.4
* SORTMTZ: new keyword VRSET.
* TRUNCATE: minor change to labels on cumulative intensity distribution
graph.
* WATERTIDY: no longer accepts the logfile output from DISTANG as input,
due to changes in DISTANG. Use the OUTPUT DISTOUT option of DISTANG
to prepare appropriate input for WATERTIDY.
* Library changes:
* New Core Libraries: new underlying C language libraries have been
introduced:
* CMTZLIB: MTZ file I/O and reflection data handling
* CMAPLIB: CCP4 mapfile I/O
* MMDB: Coordinate data handling (C++)
* CCP4_PARSER: CCP4 keyword parser
* CSYMLIB: CCP4 symmtery handling functions
* CCP4_GENERAL, CCP4_PROGRAM: utilities for providing CCP4 program
environment
* CCP4_ARRAY: resizeable array implementation
* CCP4_UNITCELL: utilities for manipulations based on cell parameters
* CVECMAT: vector and matrix manipulations
* LIBRARY_UTILS: general platform-independent utilies (date, filename
manipulations, etc)
* LIBRARY_FILE: general file I/O
* LIBRARY_ERR: functions for library error handling
These functions can be invoked from C/C++ applications (see e.g. NCONT,
PDBCUR, MTZDIFF). There are also a number of new C language libraries
providing Fortran interfaces:
* CCP4_DISKIO_F: Fortran API for file i/o
* CCP4_GENERAL_F: Fortran API to utilities providing CCP4 program
environment
* CCP4_UNITCELL_F: Fortran API to utilities for manipulations based
on cell parameters
* CCP4_PARSER_F: Fortran API for CCP4 keyword parser
* CMTZLIB_F: replicates old mtzlib.f
* CMAPLIB_F: replicates old maplib.f
* CSYMLIB_F: replicates old symlib.f
A number of old library files have been altered:
* ccplib.f: many functions replaced by CCP4_GENERAL_F
* library.c: withdrawn
* parser.f: many functions replaced by CCP4_PARSER_F
* rwbrook.f: withdrawn; replaced by Fortran API in MMDB
The Fortran APIs provided by the new libraries should match that from
the old (pre-5.0) libraries, and existing Fortran applications should be
unaffected by these changes.
The libraries build into three files: libccp4c (containing the core C
libraries in the first section above, except MMDB), libmmdb (containing
the MMDB libraries only), libccp4f (containing the Fortran and Fortran
API functions).
* Clipper: new C++ library for reflection and map handling (Kevin Cowtan)
* DNA_OUTPUT: library routines to support the DNA Project (see
http://www.dna.ac.uk/)
* FFTW: Fastest Fourier Transform in the West. Currently only used by
Clipper library.
* Monomer library: updated for REFMAC 5.2.
* New programs:
* BULK: bulk solvent correction for translation search and rigid body refinement
steps of AMoRe (A. Fokine, A. Urzhumtsev, G. Capitani, M.G. Grutter)
* DTREK2SCALA: convert integrated intensity and header files from D*TREK
into a multi-record mtz file (Gwyndaf Evans)
* EXTENDS: extend Fourier maps and compute standard uncertainty of electron
density (Phil Evans, Ian Tickle).
* MTZDIFF,MAPDIFF,PDBDIFF: utilities to examine differences between
pairs of MTZ, map and PDB files respectively (Peter Briggs)
* NCONT, PDBCUR and COORD_FORMAT: new coordinate utility programs based on the
MMDB library (Eugene Krissinel)
* PDB_EXTRACT 1.5: programs for extracting deposition data from logfiles
(RCSB)
* pdb-mode.el: major mode for editing Protein Data Bank files in
Emacs (Charlie Bond). There is also a simpler version pdb.el which
is mainly for highlighting (Martyn Winn). See also cif.el (Martyn Winn).
* TLSEXTRACT: a jiffy for extracting TLS parameters from the REMARK 3 records
of a PDB file (Jay Painter). Interfaced in Edit/Create TLS File.
* TOPDRAW: sketchpad for drawing topology cartoons of proteins
(Charlie Bond)
* Graphical User Interface:
* CCP4i version 1.3.18
* types.def: new widget types "varbutton", "postmenu", "selmenu",
"exframe_rb";
new file types "_MGPY_file" (molecular graphics script),
"_pickle_file" (MG save status), "_pic_file" (screen snapshot),
"_rlist_file" and "_sol_file" (Phaser solution files);
new MTZ label type "_mtz_label_e" (normalised structure factor).
* Help facilities: message line help is now also displayed as
"bubble help". Turn this feature off in "Configure Interface".
* Command templates (com files) can use ampersand ("&") as a
continuation character for both standard template lines and
LABELLINE commands.
* View Files from Job: when additional log and loggraph files are
output from a job, these are now grouped under submenus called
"Additional log files" and "Additional log graphs" (instead of
being in the main list of output files).
* Log file viewers: added option to use text browser to display
logfiles.
Up and down arrow keys enable single-line scrolling (Steven Ness).
* DbLockFilePid: returns pid which "owns" current database lock.
* CentreWindow: centres a window over a parent, or screen centre.
* MakeLock/LockStatus/DeleteLock/CreateLock: new procedures for
dealing with file locks.
* WriteImage: new command. Allows an image (any type supported by the
Tcl "image" command) to be displayed in a task interface.
* New module: "Graphics and Viewing Utilities" contains AstexViewer,
Loggraph, MapSlicer, RasMol (Unix only) and TopDraw.
* Amore: low resolution cutoff defaults to 15.0A, and is no longer
read from the input MTZ file. Solution files (.mr) include
SYMMETRY, CELL and RESOLUTION information in the header -
SYMMETRY from .mr file will be checked against that used for
Amore runs.
* Areaimol interface: new interface to calculate protein accessible
surface areas and area differences.
* ClustalW interface: new interface (nb the ClustalW program is not
distributed with CCP4).
* Data Harvesting Management Tool: new interface to review and
manage harvesting files produced from harvesting programs.
* Distang: removed from Program List, there is no dedicated Distang
task.
* Import Unscaled Data (combat): added option to enter wavelength.
* PrepHaData: SHELX options expanded to prepare data for either
SHELXS or SHELXD.
* Mlphare: output Hendrickson-Lattmann coefficients by default.
* Modeller: interface updated to work with either Modeller 6 (default)
or Modeller 4.
* MOSFLM interface: new interface to run MOSFLM in batch mode.
* Merge Monomer Libraries: a simpler interface has been implemented to
replace the old "AddDict" interface for merging monomer files.
"AddDict" can still be accessed via the Monomer Library Sketcher.
* Refmac5: substantial update to the Refmac interface.
* 'Old' Refmac/Protin: interfaces are retained to allow users to
review parameters from old jobs, but the tasks cannot be run as
the programs have been withdrawn.
* Scala: new option to accept observations previously flagged as
rejected by MOSFLM (ACCEPT keyword in SCALA program).
* Sketcher: 1) Report name of monomer and source file in sketcher
window; 2) Run imported CIF file through Libcheck automatically
* Edit/Create TLS File: now has "Reset" button to clear previously set
parameters. It can also extract TLS groups from the REMARK 3 records
of PDB format file. It will optionally handle TLS parameters.
* Documentation:
* symmetry.html, cheshirecell.html: new documents
* Sketcher: added to index of programs.
* Withdrawal:
* ABSURD, UNDUPL, MADLAT: programs for MADNES
* EXTEND: use MAPMASK
* REFORM: obsolete
* RWDICT: use MAKEDICT
* MSTAMP: obsolete
* PROTIN/REFMAC: use refmac5
* Examples:
* RNASE.PDB: naming of waters ("HOH") updated to be consistent with new
monomer dictionary, and with convention used in toxd.pdb: OW* changed
to O1, with one oxygen per "residue".
Summary of significant changes to CCP4 at version 4.2.1
-------------------------------------------------------
* Building etc.:
* General: running "make install" failed if executed immediately after
the configure step; now fixed.
* IRIX: fixed building of shared library by default on IRIX 6.5.
* OSF1: 1) new configure option --non_shared prevents linking executables
against shared libraries (including system libraries);
2) "-D__V40_OBJ_COMPAT -nointrinsics -D" compiler flags removed for
Tru64 V5.0.
* Mapslicer configuration: fixed problem with configure looking for Tk
library with the wrong file extension.
* Program changes:
* ASTEXVIEWER: .jar file updated to allow the viewer to run as
standalone.
* MOSFLM: version 6.2.2
contains fix for R/H3x problems.
* REFMAC5: version 5.1.24
* SCALA: version 3.1.9
* Library changes:
* CCIFLIB: fixed bug with passing fixed length for Fortran strings in
s/r ccp4ccif_setup_context.
* MAPLIB: five of the ENTRYs have been renames as they exceed 31
characters in length.
* PARSER: number of characters increased to prevent filename truncation
when filenames are read from the keyworded input.
* RWBROOK: fixed problem when spacegroup name is longer than space
permitted in PDB file.
* SYMLIB: increased the hashing parameter KPRI in CCP4_HASH_... routines
to 5003, to cope with maximum number of batches in SCALA (5000).
* Graphical User Interface:
* Version 1.3.8.
* General: Kill Job function updated to work under Mac-OSX and SunOS
* General: fixed problems starting help pages from KDE on Linux
* General: fixed problem with restarting task interfaces after being
closed using the Window Manager rather than the CCP4i "Close" button
* Refmac5: fixed problem with interface requesting harvesting information
in Review mode.
* Scala: new option to automatically combine all input datasets into
a single output dataset.
* Monomer Library Sketcher: 1) fixed problem with "unknown option -dash"
for Tk versions earlier than 8.3; 2) fixed problem with delocalised
and aromatic bond types not being written to bondlist.cif.
Summary of significant changes to CCP4 at version 4.2
------------------------------------------------------
* Building etc.:
* IRIX 6.5: changed to n32 compilation.
* LAPACK: the BLAS and LAPACK libraries are now included in the CCP4
installation by default. If a suitable system-specific LAPACK library
is not found at configuration time then the version from Netlib will
be built. Use the --disable-lapack configure flag to suppress inclusion
of the LAPACK library, or the --with-netlib-lapack flag to force
building of the Netlib versions.
* configure: Have added an extra keyword --with-warnings. If this is not specified
some systems will be compiled with a -w which will suppress compiler warnings
for the main suite.
* xdlmapman: now builds using a m4 preprocessor stage to allow system
dependent FORTRAN file record sizes.
* Program changes:
* ALMN: automatically checks that input files have consistent indexing,
and suggests reindexing operation if they do not.
* AREAIMOL: calculates contact areas as well as ASA; allows large probe
sizes (up to 25A radius); new MATCHUP option for use with DIFFMODE
COMPARE e.g. for different confirmations; ignores hydrogens in input
files; improved handling of unknown atom types.
* ARP_WATERS: The CCP4-distributed version of arp_warp (v5.0) has been
renamed to "arp_waters". Example scripts, documentation etc has also
been renamed accordingly.
* BAVERAGE : htmlized the output.
* COMBAT: the MTZF option now accepts F(+) and F(-) as an alternative
to mean F. MISBATCH option removed: now only outputs batches which
are present in the input file. INPUT USER option fixed (was broken).
"I" decsriptors in FORMAT statements are automatically converted to
the appropriate "F" format. Fixed incorrect lattice type setting for
centred spacegroups in MTZ files.
* DTREK2MTZ: previously, handled files incorrectly if there was no
anomalous data - this feature now fixed.
* DYNDOM: New version 1.2
* ECALC: LABIN will now take DPH/SIGDPH, new MODD keyword.
* F2MTZ: for USER defined input, "I"'s in the Fortran FORMAT
statement are now automatically changed to the appropriate "F"
descriptors.
* FFFEAR: Upgrade to version 1.9
* FFT/FFTBIG: the default axis ordering is Z,X,Y for P1, monoclinic
space groups, and space groups 16, 17 and 18, and Y,X,Z for all
higher symmetry space groups. Default map volume in FFTBIG is now
always the whole unit cell.
* GENSYM: fix to SPHER ORTHOGONAL option.
* MATTHEWS_COEF: Added keyword AUTO that will produce a table
of the possible number of molecules in the Asym unit.
** MOLREP: Molrep now uses keywords and command line options.
Also updated to verion 8.2.01.
* MOSFLM: version 6.2.1
* MTZ2VARIOUS: Added OUTPUT MAIN option.
* OASIS: new keywords RES and SIG, increased limit on number of
reflections, plus a number of bug fixes.
* REFMAC: version 5.1.19
* REVISE: Now produces graphs of the correlations between anomalous
differences for different wave lengths and the rms Dano; the
tables of ratioes of data sets split the data into 15 bins (was 10).
* SCALA: new version 3.1.4.
* Library:
* MAPLIB: Reinitialise mean and RMS density when creating multiple
maps in a single program run.
* PXXML: new subroutine library for writing XML.
* RWBROOK: s/r PDBREAD gives tries to identify ambigious atom names
like AC5* and NO4* when no element name is supplied.
* SYMOP: Hexagonal spacegroups 146, 148, 155, 160, 161, 166 and 167
are now refered to by the symbols H.
* unix.m4, vms.for, w32mvs.f: CCPOPN won't print error message for
file opening error if called with IFAIL=2.
* xdl_view: new version 4.5
* New programs:
* ABS: program to determine the hand of the heavy atom substructure
(Q.Hao)
* ACORN: ab initio procedure for the determination of protein structure
at atomic resolution (Yao Jia-Xing)
* ASTEXVIEWER: Java application for viewing proteins, ligands and electron
density maps (Mike Hartshorn)
* BEAST: Brute-force molecular replacement with Ensemble Average Statistics,
Maximum likelihood-based molecular repaclement (Randy Read)
* CIF2MTZ: program to convert mmCIF structure factors (e.g. from PDB)
to MTZ (Martyn Winn)
* FSEARCH: program to perform upto 6 dimensional molecular (envelope)
replacement search (Q.Hao)
* IAM (UNSUPPORTED): A specialised program for windows
purpose of this program is to just return the user name to std out
* PROFESSS (formally eleanorinabox): determination of NCS operators from
heavy atoms (Kevin Cowtan)
* REFINDEX: reindex dataset maximising correlation with reference dataset
(Ian Tickle). In Unsupported as only preliminary version.
* REFORIGIN: apply best origin shift to PDB atom co-ords according to
reference file (Ian Tickle). In Unsupported as only preliminary version.
* ROTAMER: list amino acids whose side chain torsion angles deviate from
Richardson's Penultimate Rotamer Library (Dirk Kostrewa)
* SAPI: heavy atom site location (Y.X.Gu, C.D.Zheng, H.F.Fan, Q.Hao)
* STGRID: modified version of STNET, produces a plot for measuring
the angular co-ordinates on a stereographic projection (Ian Tickle)
* TCL2HTML: Tcl script to convert Tcl script and CCP4i .def files to
html, with line numbering, colouring of comments, and html anchors
(Liz Potterton)
* Graphical User Interface:
* Version 1.3.7.
* Prepare HA data: includes option to apply high resolution cutoff
for MAD data (Revise RESO keyword). New option to input "native
data".
* FFT/PATTERSON tasks: upper sigma level now defaults to 100.
* New IMPORT/EDIT PROTEIN SEQUENCE task in Coordinate Utilities.
* MLPHARE task: new option to generate anomalous map. Don't allow
centric data only if anomalous difference data is used.
* REFMAC5: default for setting up restraints is now "do not check
anything".
* TRUNCATE: new option to input amplitudes (for analyses only).
* Tasks for importing data will now complain if you do not set a
project name or dataset name.
* Most tasks will get default title if you don't set one. When you
see how dull the default is, you will want to set your own.
* Selection behaviour for the job list in the main window has
changed: only last clicked item is selected. Selecting multiple items
is acheived by either ctrl-click (adds to selection) or shift-click
(add all items up to previously clicked line). Multiple items can
also be selected by clicking and dragging.
* Experimental Phasing module: "Merge datasets" task (CAD) added.
* MTZ label selection: the maximum length of menus of MTZ file labels is
now set in the "Configure Interface" window. Menus which have more than
this number of entries will be broken up into multiple columns.
* CreateLine command modified to:
1) Allow 'packing' of widgets into BLT table; 2) Use a different
naming scheme for widgets.
* Modules and Tasks: the list of modules and tasks is now read from a
modules.def file. Entries in an additional modules.def file placed in the
user's local area (e.g. $USER/.CCP4/unix/modules) will be appended to those
read from that in the main CCP4i area. The modules.def file can
be edited using the "Edit Modules File" task under the "System Admin" menu.
* Import Scaled Data: new task gives a single interface for importing data
from either Scalepack or D*trek - replaces the old Scalepack2mtz and
Dtrek2mtz tasks.
* OASIS: new task interface for phasing SIR or SAD data.
* ANISOANL, TLSANL: new task interfaces.
* modules_utils.tcl: new procedures to edit the modules.def files.
* Kill Job: modified to recursively kill all subprocesses of the script.
* Data Harvesting: the default is now to create harvesting files in the
current project directory, for tasks which support harvesting.
* PHISTATS: new task interface for phase set analyses.
* SFTOOLS: new option to generate Dano from F(+) and F(-).
* Main window: default size has been increased, so that all menu items
are visible on startup (the user can still resize it)
* AddOutputDir: new command to add a directory to the list of output "files"
from a job. The directory will not be displayed in the list of output files
but will be included in the cleanup procedure if the user deletes the job.
* SCALA: substantial changes for handling input and output datasets.
* CAD: new option to automatically check for and correct inconsistent
indexing between input files.
* XML: new xml_utils.tcl file contains procedures for handling CCP4 XML
files. Matthews and Molrep tasks will use XML to pass information
automatically if XML output is specified in preferences. NB these options
are developmental only.
* ARP/wARP: stand-alone interface has been withdrawn - get the latest ARP/wARP
suite and CCP4i interface from http://www.arp-warp.org/
* Mail CCP4: on Windows systems now calls up the CCP4 on-line help.
* Install New Task: substantially revised version allows install, uninstall and
export of new tasks. See documentation for full details.
* MAPCUTTING: new interface from Kevin Cowtan.
* DM: can specify NCS operators in a number of different ways (euler angles,
polar angle, rotation matrix or O matrix).
* WHATCHECK: new interface (Maria Turkenburg/Peter Briggs).
* File Viewers: user can set their default PDB and map viewer in Preferences.
* ROTAMER: new interface.
* Documentation:
* STNET: updated to clarify usage.
* CCP4i: extensive new documentation for all core Tcl routines.
* Withdrawal:
*
* Examples
* toxd.mtz, rnase18.mtz and rnase25.mtz now distributed as well as .na4 files.
Summary of significant changes to CCP4 at version 4.1
------------------------------------------------------
* Building etc.:
* ccp4.setup: shouldn't add duplicated entries to the PATH variable.
* cif_mmdic.lib (binary version of mmCIF dictionary) now installed
in $CLIB rather than $CLIBD.
* configure: (i) updated for OSF1 V5.0. (ii) Always builds fsplit
automatically in bindir (defaults to $CBIN) and uses this in the build.
(iii) Use --with-lapack option to include LAPACK maths libraries in
build (see MODLIB documentation).
* Program changes:
* AMORE: sorts rotation function output for improved solutions.
* AREAIMOL: TRANS keyword - search extended from +/-1 lattice vectors to
+/2 vectors
* AXISSEARCH: updated output; now uses keyworded input
(see documentation).
* CAD: new keywords DCELL and DWAVELENGTH for adding/changing dataset cell
and wavelength attributes.
Applies temperature factor as part of scaling (via SCALE keyword).
* DM: version 2.1. Major changes are: NCS operators are now output as
Euler angles plus translations; program will calculate the value of
NMER automatically if it is omitted by the user; XtalView/O files
can be output to visualise the NCS elements.
* DYNDOM: no longer sensitive to the order of the atoms in the PDB file.
* F2MTZ: added summary tags to output.
* GENSYM: new keywords SORT (specifies order output for sites) and
CHAIN (assigns chain ids).
* GEOMCALC: prints out equations of fitted planes.
* IPDISP: revised version of ipdisp script; new spdfil for PX210
detector.
* MAPMASK: new XYZLIM MATCH option takes the output map limits from
a map supplied by the user.
* MAPROT: changes to CELL, GRID and SYMMETRY keywords (now have
WORK/XTAL subkeys), to AVERAGE keyword (change to format for entering
NCS operators) and new INVERT keyword. Option to cut density from
one map and transfer to another.
* MLPHARE: fixed DCYCLE REFCYCL option (was broken); substantial
reformatting of logfile output.
* PDBSET: new NOISE option adds random shifts to selected atom
coordinates. Checks that symmetry from SPACEGROUP is consistent
with that from input PDB file. Calculates fractional, as well as
orthogonal limits on coordinate set. New suboption FILE for
TRANSFORM keyword (see documentation). Chain selections now use
ChainId, if SegId is blank then SegId is always set to ChainID on
output.
* PEAKMAX: change of defaults, residue type for output set to HOH,
default atom name to O.
* PHISTATS: new SHIFT keyword applies a fractional shift to the second
phase set - useful if two phase sets refer to different crystal
origins.
* PROTIN: now can apply restraints from one residue to (a
symmetry-related copy of) itself.
* REBATCH: new CELL/WAVELENGTH keywords.
* REINDEX: new (optional) subkeywords HKL/AXIS for REINDEX keyword,
control how the transformations are supplied to the program.
* REVISE: new RESO keyword to set maximum resolution.
* RSPS: new version 4.2 from Stefan Knight.
* SCALA: new version 2.7.5.
* SCALEPACK2MTZ: added summary tags to output.
* SORTMTZ: change of defaults, residue type changed to HOH, atom
to O.
* TLSANL: many changes associated with new TLS option of refmac.
* Library:
* CCPLIB: CCPVRS prints 15 characters from program name (was 10).
CCPFYP recognises new command-line arguments -nohtml (suppress
output of html tags) and -nosummary (suppress output of summary
tags).
* FFFEAR_fraglib: library of representative protein fragments for FFFEAR.
* KEYPARSE: new entry ParseAtomSelect supports simple atom selection
commands.
* LAPACK: source code for BLAS and LAPACK packages included from
Netlib.
* MTZLIB: new DCELL and DWAVEL records in MTZ header for dataset-specific
cells and wavelengths. New routines LRIDC and LWIDC for read/write
dataset cell and wavelength info.
* MODLIB: a number of routines have been added to the library from
various programs - see the MODLIB documentation.
* PARSER: new routine RDATOMSELECT supports simple atom selection
commands.
* RWBROOK: s/r XYZOPEN checks for consistency between PDB defn.s of
symmetry operations (taken from REMARK 290 lines, if present) and the
order in $CLIBD/symop.lib or mtzlib. s/r SFREAD2 now correctly reads
form factors for one character atom names from atomsf.lib (S, I and B
were affected) (Clemens Vonrhein).
* SYMLIB: s/r SYMFR2 now recognises real- and reciprocal-space
axis vector operations, e.g. a*+c*,c*,-b*; new s/r SETLIM_ARP
returns the ARP asu limits.
* SYMOP.LIB: fixed point groups for alternate spacegroups 1003, 1004,
1005, 2005, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015.
* XDL_VIEW: new version 4.4
* New programs:
* ANISOANL: various analyses of model anisotropic U values (Martyn Winn)
* ccp4keys: awk script for extracting keywords form a log file in a format
which can be cut and pasted into a new command file. (Kevin Cowtan)
* CAVENV: Calculates cavities in macromolecular structures (Anne Volbeda)
* CCP4MAPWISH: customised wish interpreter required for MAPSLICER. (Peter Briggs)
* COMBAT: replacement for ROTAPREP. (Alun Ashton)
* DTREK2MTZ: converts d*trek scalemerge output into MTZ format. (Jim Pflugrath)
* FFFEAR 1.2: Fast Fourier FEAture Recognition program. (Kevin Cowtan)
* FFJOIN: joins together fragments from FFFEAR. (Kevin Cowtan)
* MAP2FS: jiffy to convert CCP4 maps/masks to XtalView fsfour format. (Kevin Cowtan)
* MAPSLICER: viewer for contoured sections through CCP4 maps. (Peter Briggs)
* MOSFLM: now distributed with CCP4. (Andrew Leslie / Harry Powell)
* REFMAC5: major new version of REFMAC (Garib Murshudov). Old refmac and
protin moved to unsupported.
* ROTGEN: Simulate X-ray diffraction rotation images. (John Campbell)
* Graphical User Interface:
* Installation: CCP4i no longer requires Tcl/Tk to be built with a non-default
flag. It is best run using the bltwish interpreter.
* Monomer Library Sketcher: for graphics display of monomers, and
interface to Libcheck and the monomer geometry libraries.
* New interfaces to BAVERAGE, CONTACT, FFFEAR, DMMULTI,
DTREK2MTZ, SFTOOLS for SF analysis, SIGMAA, and WATERTIDY.
* Documentation:
* alternate_origins: lists alternate origins for different spacegroups.
* lsqkab.html: added a "known problems" section.
* symlib.html: extended section on applying symmetry operations.
* Withdrawal:
* ROTAPREP: moved to unsupported.
* Examples
* axissearch.exam: updated for revised version of AXISSEARCH.
* toxd.pdb: waters renamed to HOH O1.
* run-all: testing script in $CEXAM/unix/runnable which will
run all examples and report any failures
* tutorial2000: ccp4i-based tutorials. Old tutorials removed since
getting out of date.
Summary of significant changes to CCP4 at version 4.0
------------------------------------------------------
* Building etc.:
* configure: new options --help, --with-rxdispencer and --disable-ccif
New system linux_compaq_compilers
* etc/GFAC2PDB.COM added for VMS
* include/ccp4.setup-dist and ccp4.setup-bash: CCP4_OPEN set to
UNKNOWN by default since necessary for some programs, and this
is common practice. Beware over-writing existing files!
* lib/data: running fontpack has been moved to "make install" step,
since if a shared library is used it needs it to have been installed.
* Program changes:
* AMORE: major new version from Jorge Navaza
* AREAIMOL: default MODE is now NOHOH. Attempts to identify isolated
areas of surface (eg cavities) in MODEs NOHOH and ALL.
* ARP_WARP: ARP/wARP v5.0 - replaces "arpp".
* CONTACT: broken MODE ISUB fixed. CRYST1/SCALE cards not required except
for MODEs AUTO and IMOL. New keyword BIGSEARCH allows larger volume to
be searched for contacts under MODE AUTO. Should correctly identify H32
and R32.
* COORDCONV: extended to read *.ha format files.
* DETWIN: LABIN keyword added - program now accepts F's and I(+/-).
Performs new tests for twinning as a function of twinning fraction and
resolution - see documentation. OPERATOR keyword replaces existing
SYMMETRY keyword (which is still valid).
* DM: version 2.0.5.
* FHSCAL: can now apply scales calculated for F's to F(+), F(-), Imean,
I(+) and I(-), and warns if not all scalable members of a dataset have
scales applied. AUTO option enables automatic selection of all
scalable columns in chosen datasets.
* IPDISP: new version and new spdfils for reading packed MAR image files.
* MAPDUMP: accepts END/RUN/GO keyword as well as end-of-file.
* MLPHARE: keyword COORDS writes heavy atom coordinates to pseudo-pdb file.
* MTZ2VARIOUS: Extra LABIN columns FPART_BULK_S and PHIPART_BULK_S for
CIF output.
* MTZMADMOD: labels changed so that +/- are now (+)/(-)
* NCSMASK: new SPACING subkeyword for GRID option, to set arbitrary grid
spacing.
* PDBSET: added OCCUPANCY RESET and EXCLUDE SIDE options. Fixed broken
TRANSFORM FRACTIONAL option. New EXCLUDE WAT/HOH option.
* PREPFORM, PREPSHEL: new version as part of ARP/wARP suite v5.0.
* PROTIN: redimensioned for ARP/wARP.
* RWCONTENTS: keyword NHOH added to estimate no. of water molecules
that can be found by PX (Carugo and Bordo).
* REBATCH: A new sub keyword to BATCH, MAXWIDTH, has been added to specify
the maximum width of reflections. Those with higher widths are rejected.
* SCALA: new version 2.7.2.
* SCALEIT: can now apply scales calculated for F's to F(+), F(-), Imean,
I(+) and I(-), and warns if not all scalable members of a dataset have
scales applied. AUTO option enables automatic selection of all
scalable columns in chosen datasets.
* SCALEPACK2MTZ: Added code to insert html tags in log files.
* SFCHECK: version 5.3.4
* SORTMTZ: Added code to insert html tags in log files.
* SURFACE: prints out total accessible area after each calculation.
* TLSANL: New keyword BINPUT to specify whether Bs or Us in XYZIN.
* TOPP: topp.f, autosnd.f, toplist.f - all leading tabs changed to spaces
for compilation on AIX. Now version 6.5
* TRUNCATE: new loggraph table of centric and acentric moments for identifying
twinning. Plots of F/sigma added to falloff plots for identifying anisotropy.
Code added to check if data is anisotropic. Included a new keyword SCALE that
when provided overrides the wilson plot scale. Added code to insert html tags
in log files.
* WATERTIDY: fixed faulty oxygen atom recognition.
* WATNCS: all leading tabs changed to spaces for compilation on AIX.
* Library:
* lib/ccif: Peter Keller's ccif library for handling mmCIF
* cciflib.f: new library for handling mmCIF coordinate files. At present,
not used by distributed programs. Uses libccif.a
* harvlib.f: new library for writing data harvesting files. Used by
MLPHARE, TRUNCATE and RESTRAIN. Uses libccif.a
* lgglib.f: all leading tabs changed to spaces for compilation on AIX.
* rwbrook.f: new routine NUM_EXPECTED_WATERS. Changes to XYZOPEN (issues
warnings if no CRYST1 or SCALE cards are found in input PDB file).
* sc_radii.lib: atomic radii library file for new SC program.
* symlib.f: new s/r CALC_ORIG_PS.
* symop.lib: one line per symmetry operation. Some minor corrections.
* New programs:
* MOLREP: automated program for molecular replacement, from Alexei Vagin
* OASIS: program for breaking phase ambiguity in OAS or SIR, from Quan Hao
* RWCONTENTS: promoted from unsupported.
* SC: program to analyse shape complementarity of molecular interfaces
* T_SHIFT: part of ARP/wARP suite v5.0.
* Documentation:
* ccplib.html: new documentation for the CCP4 utility routines in CCPLIB.
* diskio.html: new documentation for the I/O library routines in DISKIO.
* INDEX.html: new File Formats section. Includes pdbformat.html taken
from original rwbrook.html, and mmcifformat.html for mmCIF and CCIF.
Descriptions of MTZ and map formats can be found in Library section.
* keyparse.html: new documentation for the KEYPARSE library routines.
* library.html: new documentation for the routines in LIBRARY.C.
* makedict.html: now has hints for making PROTIN dictionary entries.
* modlib.html : new documentation for the CCP4 maths routines library
MODLIB.
* parser.html: new documentation for the PARSER library routines.
* unix.html: documentation for the library routines in UNIX.M4, VMS.FOR and
W32MVS.
* Withdrawal:
* Examples
* arp_warp.exam: updated version of old "arpp.exam" using ARP/wARP v5.0
* cad_rnase.exam: example using CAD to add project and dataset
information to an mtz file.
* makedict.exam: two examples of using MAKEDICT.
* mtzMADmod.exam: example of adding F+/- columns to a file.
* oasis_oas.exam, oasis_sir.exam: two examples for OASIS.
* protin_substrate: updated to use MAKEDICT.
* rebatch.exam: A new example using the aucn data.
* rnase.pdb: terminal oxygens renamed from "OE" to "OXT",
in line with the PDB standard.
* sc.exam: two non-runnable examples for SC.
* sfall.exam: three simple examples of running SFALL.
* surface_rnase.exam: example of running SURFACE on rnase data.
* toxd.pdb: terminal oxygen renamed from "OE" to "OXT",
in line with the PDB standard.
Summary of significant changes to CCP4 at version 3.5
------------------------------------------------------
* Building etc.:
** configure script has new system irix64 for 64 bit compilation on
SGI with irix 6.*
** configure script has new option --with-x for sgi/linux/and osf1
will compile the xwindows progs
** ccp4.setup-dist/bash : has PLOT_COMMAND and PRINT_COMMAND that need
to be set for XCCPJIFFY's to work correctly.
* duptree: new version using relative pathnames. Original behaviour can
be obtained by using the -a (absolute pathname) flag.
* Makefile.in in $CCP4 has new JAVATARGETS target, currently only used
for moving java executables JLogGraph.class and JLogCanvas.class from
$CPROG to $CBIN upon "make install".
* x-windows/XCCPJIFFY: added IRIX_6 option (actually the same as IRIX_5
but clearer to have it explicit)
Irix 6.5 needed a section to itself.
** x-windows/XCCPJIFFY: added Imakefile.in
* Program changes:
* AREAIMOL: substantially updated version now also incorporates DIFFAREA,
RESAREA and WATERAREA. See documentation.
* CAD: new keywords PNAME/DNAME for adding dataset info. Will now swap
F+/F- or I+/I- columns on changing hand of indices.
* CONTACT: substantially new version.
* DM: Version 2.0.3
Output log file enhanced if viewed through web browser.
* ECALC: now uses absolute differences to calculate E. EXCLUDE keyword
added. Extra column SIGE written to output mtz. Scatter Plot removed
from the log as the info is already in the tables.
* FFT,FFTBIG: XYZLIM ASU option automatically sets map limits to correct
asymmetric unit.
* FHSCAL: Modification from Richard Kingston to process F+/- columns.
* FREERFLAG: New keyword SEED to seed random number generator using
current time. Systematic absences also assigned a FreeR flag (no longer
flagged as missing). OLDFREE keyword removed.
* HKLVIEW: new -d option specifies resolution limit.
* ICOEFL: LABOUT and END keywords fixed.
* IPDISP: extra spdfil files added for new detectors. Some options
for existing detectors updated.
* MAPMASK: SYMM now over-rides map file header. Optional MODE keyword
added.
* MTZ2VARIOUS: OUTPUT CIF now gives correct spacegroup format. OUTPUT
CNS and OUTPUT SCAL (for SOLVE) added.
* MTZDUMP: limits output in "resolution" column have been corrected.
* NPO: subkeyword FRAC added to existing SECTNS keyword.
* PDBSET: SPACEGROUP and EXCLUDE HEADER options fixed.
* PEAKMAX: New output option FRAC added. Existing output PEAKS option now
writes to logical name PEAKS. Program now outputs the height/rms(density)
(instead of height) in output files and in logfile. Some formats changed
in logfile and OUTPUT BROOKHAVEN.
* PROTIN: fixed problems with being unable to assign a SPECial distance
between atoms in multiple confirmations, and with checks only for
distances being applied for first residue of non-protein chains.
* REFMAC: version 4.0.2 with anisotropic refinement
* REINDEX: new version - see documentation.
* ROTAPREP: option SCAL_NM2 for new SCALEPACK output.
* RSTATS: functionality of RESOLUTION keyword changed. All reflections
now written to output mtz.
* RWCONTENTS: extended to give estimates of the fraction of the unit cell
which is empty or which contains solvent. Also calculates Matthews
coefficient.
* SCALA: new version 2.5.5.
Output log file enhanced if viewed through web browser.
* SCALEIT: SCAT keyword to include scatter plots in log files. Default
is now not to.
* WILSON: can read in intensities or amplitudes.
* Library:
* lgglib.f: routines from Guoguang Lu
* libhtml.f: new library routines for adding HTML tags into program output
so that log files can be viewed as HTML documents. Associated java code in
JLogGraph.java (compiled as JLogGraph.class and JLogCanvas.class) allow
log graphs to be embedded and viewed directly through Java-enabled HTML
browser.
* library.c: new routine hgetlimits for harvesting
* maplib.f: descriptive names for subroutines now available alongside existing
subroutine names. New routines CCP4MAPHEAD, CCP4MAPIN and CCP4MAPOUT added.
* modlib.f: new matrix multiplication routines MATMULNM and MATMULGEN.
* protin.dic: IUM residue entry revised with more comprehensive list of elements.
* rwbrook.f: routines XYZADVANCE and WBCELL now print spacegroup name (if available)
after cell info of CRYST1 card. New routine WBSPGRP used to set spacegroup name.
RBSPGRP now returns spacegroup name automatically left-justified. New routine
RWNOHEAD suppresses output of CRYST1 and SCALE cards.
* symop.lib: extended version of symop.lib, containing additional alternative
spacegroup names. Groups 1017, 2017, 2018, 3018 added. (Old symop.lib
retained in symop_old.lib)
* symlib.f: new routine MSYMLB2 to return CIF-style spacegroup name. New routine
MSYMLB3 returns most detailed spacegroup name, checks all symmetry operators
in spacegroup form a closed set, and derives the pointgroup from the existing
subroutine PGDEFN (ignoring that given in $SYMOP). New routine SYMTR4 converts
matrices to symmetry operations more consistently than existing SYMTR3.
Routines SETUP, LOOKUP and ZEROIT renamed (now preceeded by "CCP4_HASH_"), and
relevant programs altered (POSTREF, REBATCH, SCALA).
* $CLIBD/protin.dic: HOH added as residue to fit pdb format
* New programs:
* DETWIN: detwins merohedrally twinned data.
* DYNDOM: Program to Determine Domains, Hinge Axes and Hinge Bending Residues
in Proteins where Two Conformations are Available. From Steve Hayward.
* FINDNCS: detect NCS operations automatically from heavy atom sites.
From Guoguang Lu.
* MTZMADMOD: Jiffy for converting between F+/F- and F/D
* TOPP: an automatic topological and atomic comparison program for protein
structures. From Guoguang Lu.
* WATNCS: Pick waters which follow NCS and sort out to NCS asymmetric unit.
From Guoguang Lu.
* Documentation:
* ipdisp.html: contains list of available spdfils and new section on creating
and custominsing spdfils.
* libhtml.html: documentation for new libhtml.f library subroutines.
* protin.html: contains example with RNA.
* symlib.html: documentation for symmetry library subroutines in symlib.f.
* freerunique.html, reindexing.html, scalechoose.html, twinning.html: new
general documentation.
* Withdrawal:
* DIFFAREA, RESAREA and WATERAREA all now incorporated into AREAIMOL.
* Examples
* areaimol.exam: examples for new version.
* toxd.pdb: Chain names added and TER card at end of protein
* ncsmask.exam: one run of pdbset removed as toxd.pdb now has chain ID
* arpp.exam: pdbset run ajusted. extend replaced with mapmask.
* watpeak.exam: pdbset run ajusted.
* watertidy-3shells: pdbset run ajusted.
* sortwater.exam: pdbset run removed.
* bplot.exam: resudue names changed to include CHAIN ID.
* f2mtz.exam: adjusted XPLOR example to accept output from new mtz2various.
new example added.
* mtz2various.exam: extra example of OUTPUT USER with DUM labels.
** rnase : $CEXAM/rnase/ directory added with data/scripts/pdb
see $CEXAM/rnase/README for details
Summary of significant changes to CCP4 at version 3.4
------------------------------------------------------
* Building etc.:
* duptree: new script for setting up multiple installations
* C programs: changes to PLTDEV, BINSORT and SOLOMON so that they should
compile on HPUX.
* linux/g77: all programs should now compile with linux/g77
* x-windows: trial configure and Makefile.in for IRIX, OSF1 and LINUX.
* Program changes:
* AREAIMOL: now takes keyworded input.
* FFT/FFTBIG: will now print out Harker sections.
* GETAX: New version - g77 compliant.
* NPO: now can take XYZIN again! New version from Eleanor Dodson.
* PROCHECK: New version - now g77 friendly.
* SCALA: version 2.4.2 included
* SIGMAA: subsubkeywords LOW and HIGH of COMB RESO removed, since
of little use and didn't work properly.
* SORTWATER: Duplicate waters (after applying symmetry operators) are removed.
* TRUNCATE: FALLOFF option to visualise anisotropy (Yorgo Modis).
* VECTORS: now sets Bfactors to 1.0 to fit in with NPO
* Library:
* ccplib: minor y2k fixes.
* rwbrook: new routines RBRORF2, CVANISOU, RBSPGRP.
* symlib: changes to SYMTR3 to allow calculation of Harker sections,
new ENTRY CENTPHS to return PHASE class.
* New programs:
* BAVERAGE: promoted from Unsupported (now keyworded).
* BPLOT: promoted from Unsupported.
* MAPDUMP: from old unsupported PRMAP.
* RANTAN: Direct Method module for the determination of heavy atom positions
in a macro-molecule structure or to determine a small molecule structure.
* SFCHECK: Structure factor checking
* SFTOOLS: Reflection data file utility program from Bart Hazes.
* DMMULTI: multi-xtal density modification package
* Documentation:
* html versions of dm_ncs_averaging and dm_skeletonisation added.
* arppdoc.ps removed - contents included in arpp.html
* $CCP4/manual/procheck/manual.ps removed since out-of-date. New
comprehensive html version.
* Withdrawal:
* ABSCALE: obsolete
* AGROVATA/ROTAVATA: replaced by SCALA
* ENVELOPE: replaced by DM
* EXTEND: moved to unsupported, replaced by MAPMASK.
* FLATMAP: replaced by DM
* PROLSQ: replaced by REFMAC
* PSAVER: replaced by NCSMASK/DM.
* RESLICE: replaced by MAPMASK.
Summary of significant changes to CCP4 at version 3.3
------------------------------------------------------
* Building etc.:
* $CCP4/Makefile.in: makeman script automatically runs when typing make
from $CCP4.
* $CHTML/makeman.csh: man pages can effectively be generated by running
this script. Symbolic links are made from $CCP4/man/cat1/ to the $CDOC
files which are then viewable by `man`.
** $CINCL/ccp4.setup: $CMAN has been removed and $CHTML = $CCP4/html has been
added. $CCP4_BROWSER added - it is to be the path and name of an html browser
to be used for viewing ccp4 documentation. ccp4help alias added to run
$CCP4_BROWSER with file $CHTML/INDEX.html
* MAKEFILE.COM: "DEC Fortran" is no longer a valid test between Alpha and
VAX. Test has been changed.
* MAKEFILE.MMS: has been removed as it was out of date. Nobody noticed so
perhaps everyone is using the makefile.
* MOSFLMBITS.COM: has been removed because it is no longer needed.
* configure: changed building of shared library for OSF1. Also, `pwd`
changed to `pwd`/ as there may have been problems installing the shared
library. The -with-mosflm option is being removed. The library routines
are not need for the new version of MOSFLM. --tmpdir=DIR option added.
g77 is now the default compiler for linux - not fully tested.
* Program changes:
* AGROVATA: program labels changed from I+ to I(+) etc. to be consistent
with SCALA and TRUNCATE.
* BONES2PDB: now recognises BONES_ATOM_XYZ and BONE_ATOM_XYZ as valid
datablock headers, as well as SKEL_ATOM_XYZ.
* CROSSEC: input now fully keyworded.
* * DM: have version 1.8.1 from Kevin. The 'solvent flipping' option has been
removed and solvent flattening and histogram matching are compulsory.
* ECALC: now has an option "SNB" which outputs E's in the format
Shake-and-Bake reads.
* FFT: P222 and P2221 have been removed as valid FFTSPACEGROUPs becuase of
errors in calculating the maps. The C222 (21) routines are now working
properly.
* FFT,FFTBIG: there was a chance that F could be negative if bias removed.
Fixed so that F > 0. ABCOEFFS file altered to avoid mis-interpretation.
* FHSCAL: now has an option "CENT" which uses only centrics for scaling,
which may be more accurate in space groups with a lot of centrics such
as tetragonal
* HKLVIEW: changes to handle MNFs. Partials were not added properly, now
fixed.
* MAMA2CCP4: automatic format identification didn't work for VMS. Fixed.
* MLPHARE: format error when using 'PRINT RMSF RMSE' fixed. Problem with
FOM out of range 1.0 - 0.0 fixed. New APPLY keyword for applying
refined scales to derivative data. Maximum number of derivatives
increased to 20. Reflections could have been rejected incorrectly if
data was anomalous but had no deltaF. Now fixed.
* MTZ2VARIOUS: new option INCLUDE FREER to select just freer set.
If FREE column included and not used in INCLUDE/EXCLUDE options, then
OUTPUT TNT will now output it.
* MTZDUMP: new HEADER keyword, with corresponding -e option to mtzdmp.
* * NCSMASK: problem with keyword 'OVER' removed.
* * NPO: fixed one bug with USEORTEP. Probably others. FILE keyword removed
now must assign coordinate input to XYZIN1, XYZIN2 ...
* OVERLAPMAP: END keyword added, error in xloggraph output removed.
* PROTIN: New CONTACTS subkeywords for extended anti-bumping checking.
New SPECIAL SYMM and CHNTYP SPECIAL RESN <> TO <> keywords.
* POSTREF: keyword ABSORPTION replaced with INSCALE
* REBATCH: DETECTOR option added, for use with SCALA. Added BATCH [ALL] option.
* * RESTRAIN: New Version 4.5 added.
* ROTAPREP: an extra input option has been added MTZI. Also, new keyword
DETECTOR has been added for use with SCALA. It now also outputs MNFs in
columns which are not appropriate (eg XDET, YDET). CELL keyword will
override the cell read in from DENZO or MTZ formats.
* * ROTAVATA: program labels changed from I+ to I(+) etc. to be consistent
with other programs.
* * SCALA: new version 2.3.1 from PRE. Has made AGROVATA and ROTAVATA
obsolete.
* SCALEPACK2MTZ: output labels changed from I- to I(-) etc. to avoid
problems with parser. Missing data treatment added. New keywords
ANOM and CELL.
* SCALEIT: checks on keyword combinations of ANALYSE, SCALE and REFINE
now applied. Anisotropic scale was not applied when using SCALE. Also, if
SCALE card used then the scales specified are not refined.
* SFALL: checks to see if symmetry assigned (not all options have HKLIN).
* SIGMAA, TRUNCATE, WILSON: typo found in the subroutine LSQ. Effects the
fitting of the straight line through the Wilson PLot.
* SOLOMON: can now read various O mask formats, can decide automatically
which. However, will only output CCP4 masks.
* SORTWATER: corrected syntax of NCS ... SAME command
* SURFACE: FORMAT BNL renamed PDB.
* * TRUNCATE: input columns IW(+) etc. now not used (scalepack2mtz doesn't
produce them). Corrections to MNF handling. Input labels now I(-)
instead of I- etc. ANOM OFF now works. It has been changed to use form
factors from atomsf.lib rather than an internal table. This means that
more atom types can be catered for. The values are different from before
so there will be slight differences from earlier version of truncate.
* Library:
* MTZLIB: there was an inconsistency between program labels being case
insensitive and file labels being case sensitive. Now both are case
sensitive. WARNING; program labels must be in upper case when specified
in LABIN.
* RWBROOK: these routines have been changed extensively because of the
proposed change in format for co-ordinate files. This should be
transparent to users (although some programs have been altered, check
documenation) but developers will need to conform to the new routines.
More details can be seen on the Web in the Developers Section.
* New programs:
* ARPP: AUTOMATED REFINEMENT PROGRAM from VICTOR S. LAMZIN.
Note that "arp" has been renamed "arpp" to avoid conflict with unix command.
* GETAX from Clemens Vonrhein. Real space searching for rotation axis of
a D<n> or C<n> multimer (<n> = 2,3,4,5,6,...).
* OMIT from Bauke Dijkstra and Fred Vellieux. Calculate omit maps
according to procedure of Bhat.
* RDENT: create dictionary entries for Restrain from PDB file.
* STNET moved from unsupported
* REVISE: program to generate normalised anomlous scattering factor
magnitudes from MAD data (Yao Jia-xing).
* wulff.ps added to 'aggregated' stuff, for generating Wulff
net (Ian Clifton).
* Documentation:
* All program documentation has been converted to html. These are now the
master copies and the plain text docs are generated from them. Man pages are
formally dead. If you set up a cat1 directory pointing to $CDOC then you can
continue to use the man command. A "whatis" file is distributed in
$CHTML so that you can still use man -k or apropos.
* $CCP4/man and $CCP4/unsupported/man have been removed.
All files are now in $CDOC and $CHTML.
* $CHTML/matthews_coef: unforunately the initial formula for Vp was
incorrect and has now been corrected.
* Some new flow charts added to manual.
* Examples:
* $CEXAM/unix/runnable/scalepack2mtz.exam added.
* $CEXAM/unix/runnable/agrovata.exam and $CEXAM/unix/runnable/rotavata.exam
removed. If you need an example, you should be using scala.
* $CEXAM/tutorial: the MTZ files which are part of the tutorial are now
distributed as NA4 files. Problem with file names in MR tutorial fixed.
* All *.sh have been converted to *.exam files because of the problems with
viewing these with netscape.
* Withdrawal:
* $CETC/cman: this utility has been withdrawn, as the man pages are now dead.
* $CLIBS/chelp.c and $CLIBS/graflib.f will be moved to the 'mosflm-bits'
directory on the anonymous ftp server. They are not required for the new
version of MOSFLM.
* ABSCALE: moved to unsupported directory.
* AGROVATA: moved to unsupported directory. Function has been taken over
by SCALA.
* PLANES: was unsupported, now withdrawn. Functionality is covered
by GEOMCALC. PLANES hasn't been converted to use new RWBROOK subroutines,
but if you want the code to hack, call us at DL.
* POSTREF: moved to unsupported directory.
* PROLSQ: moved to unsupported directory. Use REFMAC.
* ROTAVATA: moved to unsupported directory. Function has been taken over
by SCALA.
* SUPERPOSE: function duplicated in both LSQKAB and POLYPOSE.
* DERIV : was unsupported, functions duplicated in SFALL.
Summary of significant changes to CCP4 at version 3.2
------------------------------------------------------
* Building etc.:
* $CCP4/x-windows/XCCPJIFFY/Imakefile: compiler options for HPUX sent
by Morten Kjeldgaard.
* $CCP4/x-windows/xdlgjk/Makefile: added install and empty-targets
procedures, in line with $CPROG. Added MAKEFILE.COM
* $CPROG/MAKEFILE.COM: procedure for Solomon was causing a warning but
compilation was not affected. This has been fixed to eliminate warning.
Solomon compiled with case sensitivity.
* Compilation of C code changed due to library.h.
* configure: because of problems with the optimisation the default is
now O1 for OSF1. IRIX6.2 section added. Warning messages have been
surpressed for IRIX5*, HPUX A.09.* and OSF1.
* Program changes:
* AMORE: if the B for an atom is zero or below then it is reset to 20.0. A
message is printed if this is the case.
* BONES2PDB: latest version from KDC on 7/10/96.
* DM: lastest version from KDC on 7/10/96.
* ECALC: resolution keyword is now acted upon.
* F2MTZ: calls to fatal were incorrect.
* FFT: keyword FILL didn't do anything - fixed. New keyword GRID SAMPLE to
specify the sampling grid as a fraction of the resolution. FFTs in P2 did
not work properly and has been removed. P1 should be used instead of P2.
* FHSCAL: labels DANO and SIGDANO changed to DPH and SIGDPH to be consistant
with SCALEIT.
* IPDISP: spdfils have been changed for MARs. -Ms is now a bigmar with
squashed format. -Mo has been removed but is equivalent to -M. -m small
mar in original format. All these are big endian. -V is the same and
now -v is small mar from VAX i.e. little endian.
* MAMA2CCP4: latest version from KDC on 7/10/96.
* MAPMASK: latest version from KDC on 7/10/96.
* MAPROT: latest version from KDC on 7/10/96.
* MLPHARE: problems with printing MNFs when monitoring reflections fixed.
* MTZ2VARIOUS: typo in defining external function was causing compilation
problems. Now fixed. EXCLUDE FREER will now exclude any freeR subset. Any
FreeR sub-set in the MTZ file can be output as the FreeR set to XPLOR,
SHELX. Dummy columns IDUM?? have been added, these will output as integers
in USER mode. An mmCIF file of the reflection data and associated data
can now be generated. XPLOR output changed to output SIGMA instead of SIGM.
* MTZDUMP: FORMAT keyword introduced so that the reflection list can be
output in a certain format. Resolution limits are applied to the overall
statistics. Missing reflections are flagged with '?'. Ranges are now calculated
for the partial statistics tables (STATS keyword).
* MTZUTILS: the UNIQUE option data from file 2 was output instead of file 1.
Bug now fixed. Associated columns properly scaled with SCALE option.
* NCSMASK: latest version from KDC on 7/10/96.
* POLYPOSE: Bugs fixed so that default values work if FIX and INCLUDE not
specified.
* POSTREF: the column label 'ABSFAC' and 'SIGABS' have been changed to
'SCALE' and 'SIGSCALE' in order to work with output from SCALA.
* PROCHECK: a write statement in PPLOT was over 132 characters. Changed
the write to avoid this. Only a problem with VMS.
* PROTIN: +PROLSQ & REFMAC the format of the PROTOUT file has changed so
that the files will not be compatible with last version. Change is so that
residue numbers up to 9999 are allowed.
* REFMAC: Output FOM as well. Made P1 default symmetry. Now supports cubic
spacegroups. Defaults have changed since last version please read the
documentation.
* RESTRAIN: updated to version 4.3.5 from Ian Tickle. Isotropic Bs are
written out properly when outputing aniso. Us.
* ROTAPREP: the way the batches are handled is now more consistant. NBATCH
keyword has been removed, the number of batches is taken from the file
where appropriate. MISBATCH keyword added to specify missing batches.
* SCALEIT: interesting stats. on large isomorphous/anomalous differences
produced for REFINE and ANALYSE modes. Normal probability analysis now
seperates centrics and acentrics. Now outputs Kraut scale instead of
reciprocal.
* SIGMAA: problem with missing FC sorted.
* SOLOMON: CCP4 masks were not being read properly, now fixed. O style
rotation and translation operators do not have to have the header line.
Problems have have been caused when averaging using CCP4 masks, now
resolved.
* TRUNCATE: divide by zero problem fixed. The output now contains H K L
F SD Dano SD F+ SdF+ F- SdF- Imean SD I+ SdI+ I- SdI-. Also, scaling with
the Wilson plot is compulsory.
* XDLMAPMAN and XDLDATAMAN: removed system dependent routines. Altered the
menu and io windows so there are sized flexibly. Also, added command line
qualifier so font for menu can be changed.
* New programs:
* MAKEDICT: will produce TNT or PROTIN dictionary entries from a PDB
or PROTIN file.
* MATTHEWS_COEF: written by Misha Isupov to calculate the Matthews
coefficient given the cell, symmetry, number of atoms etc..
* RASMOL: RasMol 2.6 (unix and VMS versions) are now distributed with CCP4.
* SCALEPACK2MTZ: Convert SCALEPACK output into an MTZ file. It then must
got through TRUNCATE to convert to Fs.
* Library:
* $CLIBD/(no)chiral_pep*.dic: correction to ARG sidechain.
* $CLIBD/atomsf_neutron.lib: Change atomic number of D to 101 to bring
into line with RBROOK.
* chelp.c: some irregularities fixed.
* chelp.h: machine dependent stuff now in library.h.
* library.c: integer type was incorrectly defined for Big-endian
machines with CONVERT_FROM set.
* library.h: has been created from library.c. This will contain the machine
dependences required for all C programs.
* mtzlib.f: bug in LRREFL fixed; affected BIOMOL programs.
* rwbrook.f: s/r SFREAD moved here from AMORE,MLPHARE,REFMAC,SFALL
* Documentation:
* RSTATS: document brought in line with prog. FREE keyword added.
* Tutorials: a new set of tutorials have been made in five main areas:
MIR, MR, refinement, density moification and MAD. These procedural scripts
can be found in $CEXAM/tutorial.
* html versions of the documentation for most of the main programs are
in $CCP4/html Point your browser at $CCP4/html/INDEX.html
* x-windows/doc: file names have been changed but essentially the *.txt
files are similar to the old *.doc* files.
* Withdrawal:
* ROTAVATA: will be unsupported in release 3.3. SCALA will become the
recommended program.
* PROLSQ: will be unsupported in release 3.3. REFMAC will become the
recommended program.
Summary of significant changes to CCP4 at version 3.1
------------------------------------------------------
* Building etc.:
* configure: fftbig, tracer and amore have individual compile
flags for AIX. OSF/1 optimisation reduced to -O1; problem
with FFT SCALE card suggests compiler problem.
* include/environ.def,default.def: refmac files added.
* CPROG:MAKEFILE.COM: typo in linking of refmac corrected.
* Program changes:
* General: A number of programs were found to close files on program
termination. This may cause problems on some machines. Here
is a list of progs. that were changed (not all programs have been
checked): abscale, act, agrovata, almn, contact, coordconv, crossec,
extend, f2mtz, fft, fftbig, gensym, geomcalc, hgen, hklplot, icoefl,
mlphare, mtz2various, mtztona4, npo, pdbset, peakmax, polarrfn, prolsq,
protin, rfcorr, rotaprep, rstats, sortwater, undupl, vectors, volume.
* FFTBIG: compiler/runtime problems caused by undefined LNAN fixed.
* FHSCAL: problem with eof on input corrected. LIST can take a no. > no.
of refls. without crashing. Statistics for old style MTZ the same as
new.
* FREERFLAG: systematic absences are now not assigned a freeR flag but
are flagged as missing. When using the COMPLETE keyword the freeR flag
information is taken from the MTZ file and not the keyword input.
* HKLVIEW: minv replaced by minv3 because of routine renaming in
modlib.f (see 3.0).
* MAMA2CCP4: problem fixed wrt quotes in call to ccperr.
* MLPHARE: compiler problems caused by undefined CCPNUN fixed.
* MTZ2VARIOUS: keyword NaN replaced by MISS.
* MTZDUMP: missing reflections are printed as "MNF". The VALM keyword
has been removed.
* PROCHECK: now the first atom in *.new is printed only once. CONVAX
has now beenons are printed as "MNF". The VALM keyword
has been removed.
* PROCHECK: now the first atom in *.new is printed only once. CONVAX
has now been added to distribution.
* PROTIN: error in handling of multiple disordered planar groups fixed?
Atoms now must have VDW radii defined. Hence, changes in dictioaries.
* REFMAC: several fixes.
* ROTAPREP: can now convert user-defined format to multi-record MTZ
file (INPU USER).
* SOLOMON: (solomon.c) parameters for rbfro1 were undefined.
* STEREO: keyword CONSTRAIN could not be used, now working.
* Library:
* SYMLIB: maximum no. of symmetry operators increased to 192. Now
consistent with MTZLIB. Error in handling P2 C unique corrected.
* $CLIBD/protin.dic: all atoms have VDW radii defined. Changed OXT and OE
for NFORMYL and NACETYL so they are consistant with OT.
* $CLIBD/protin_jp.dic: extra terminal atoms (OE, OXT) added to terminal
residues similar to protin.dic.
* $CLIBD/protin_vl.dic: extra terminal atoms added to terminal
residues similar to protin.dic.
* Examples:
* *.log-dist: all files except completedata and na4tomtz have been removed
from the $CEXAM/toxd area. Some files have been added to the
$CEXAM/unix/runnable area.
* Solomon.sh: incorrect keyword was changed. Error in reading map files
corrected.
* $CETC/uniqueify: original cell now retained rather than rounded up version.
Problem with some refls. not being assigned a FreeR flag overcome.
-f switch modified to accept <label> argument. -p <fraction> switch added.
* $CETC/UNIQUIFY.COM: added. VMS version of uniqueify
* Documentation:
* hgen: included this time.
* mtzutils: RZONE described correctly now.
* Solomon: MULSOLV keyword incorrectly referenced in the doc as
SLVMUL.
* mtzmnf: clarified that columns not specified in LABIN are output
unchanged.
* unique: improved description of uniqueify script.
Summary of significant changes to CCP4 at version 3.0
------------------------------------------------------
* Building etc.:
* ccp4/etc/PROCHECK*.COM: hopefully the problem with PRODIR$ is now
sorted.
* XCCPJIFFY: SUNOS_5 added to Imakefile, SUNOS_4 hints in comments.
* Irix6 configuration is provided, your mileage may vary -- it did for me.
Feedback still wanted.
* Program changes:
* AMORE: The HKLM keyword has been reinstated. Default NM=25. Fix: all
0kl reflections of table were 0. Keyword END now accepted. Fix possible
problems with inverse FFT due to dimensioning error. Fix failure to get
FFT prime factors right. Less likely to overflow limits on HKL. SORTFUN
can generate a table -- enables use of Es for TRAFUN. Maximum value for
TRAFUN NMOL <nmol> increased to 9. The ROTATE NSR keyword reinstated.
* CAD: The scale factor is now applied to the correct columns and not to
inappropriate ones like phase.
* DM: correct multi-domain averaging bug. DM 1.6 now current version.
* ECALC: Use LABIN and LABOUT rather than FOBS/ISODIFF -- incompatible
change. Introduced SCALE card to scale F and F2OR.
* F2MTZ: Deal with SHELX free R.
* FFT/FFTBIG: A new keyword has been added FILLIN which substitutes F2 for
F1 if F1 is missing. This only works if the MTZ file has been properly
converted to Missing Number Flags.
* FHSCAL: Resolution card added so that data can be truncated in output
file.
* FREERFLAG: Default semantics of free R column changed, along with its
type: it's picked from a set of integers, allowing full cross-validation.
An existing free R set may be completed when reflections are added (only
if using missing data conventions).
* HKLPLOT: Redimensioning, improved output.
* IPDISP: spdfil.mar_n now image type "bigovf", to indicate overflow
table. ipdisp -m option points to spdfil.mar_n (bigend rather than
littleend image)
* MLPHARE: Phasing power was printed as 0.0 with PRINT AVE. SCALE FP option
removed. Resolution in Angstroms is added to tables but not plotted on
xlog-graphs. SCRIPT keyword will produce either a VMS COM file or unix
script with refined heavy atom parmeters. Ensure Angstrom coordinates are
in PDB format - Orthogonal code 1. Will now produce NaNs for unphased
reflections.
* MTZ2VARIOUS: Remove RESTRAIN input type (never actually necessary
since restrain can specify the input format) now restrain reads MTZ. OUTPUT
USER will now output DP and SIGDP. For USER the ordering of the columns is
taken from the ordering on LABIN not LSPRGI table. If reflection record
has NaN, by default reflection not output. NAN keyword will output them.
* MTZDUMP: Missing data identified through MNFs. File statistics table
now gives single "Mean" and "Mean abs." which is calculated from all
non-missing data in a column. LRES option added to list resolution.
More flexible statistics available via STAT keyword.
* NA4TOMTZ: Fix incorrect call of `qnan'. (Unlikely to have caused problems
before missing data changes.)
* NPO: colours are now consistant with those defined in XCCPJiffy. CHAIN
sub-keyword removed. Input handling improved a little. JOIN RADII HBOND
now works as it should. Msecst has been reinstated. Can now have maps
stacks like 3,5,7 or 5,10,15 etc.. RADII BOND ALL fixed.
* OVERLAPMAP: changed code for EXCLUDE option. Will have non-zero point in
mapout if |grid_point| < 1.0e-06 in map1.
* PDBSET: new keywords added EXCLUDE HEADERS, EXCLUDE HYDROGENS and SEQUENCE
[PDB|SINGLE].
* PHISTATS: output improved + documentation.
* PLTDEV: `-pen' option now works (e.g. for colour PostScript). Colours
are now consistant with those defined in XCCPJiffy.
* PROLSQ: the keyword RTEST has been reconstructed. Now you can only have
RTEST -1|0. This means that you cannot recalculate structure factors i.e.
RTEST +1.
* PROCHECK: Updated to v. 3.3.2 plus fixes.
* PROTIN: Didn't find contacts between the same residue on symmetry related
molecules; error in packed symmtery number caused some contacts not to be
picked up by prolsq; increase some dimensions; error in checking special
inter-chain distances; no longer monitors short hydrogen bonds. Can now
use atom names which represent ions e.g. Fe+2, U+6 etc. Non-protein residue
atoms all assigned as side-chain not as main-chain and side-chain.
* RFCORR: arrays for PARSER redimensioned to avoid problem with TITLE. Polar
angles are output correctly when have exact 2-fold axes.
* ROTAPREP: Format for SCALEPACK options changed from F8.1 to F8.0. Also,
updated man page.
* ROTMAP: the table printed after the OUTPUT ... keyword was incorrect, now
fixed.
* RSPS: Failed to handle SGs with Patterson symmetry groups 143-145.
* RSTATS: OUTPUT ASIN changed to LABOUT ALLIN. PROCESS FOBS should work.
Ranges in F applied to Fobs only. Xloggraph altered and new column added
ln(<Fo>/<Fc>) v resolution.
* SCALEIT: failed for more than 9 derivatives
* SFALL: Reads formfactors automatically if not specified, but still no way
to distinguish Fe Fe+2, Fe+3 except to enter manually. Obsolete keywords
removed.
* SIGMAA: `PARTIAL DAMP' didn't work. HLAC ... HLDC now output correctly.
Map cofficients can now be constructed for missing reflections.
* SORTMTZ: now not only does there need to be an equal number of columns in
each file but the column types must be equal.
* SURFACE: trapped uninitialised variable, important for output.
* TRACER: prog. now works correctly.
* TRUNCATE: MTZ columns were potentially scrambled for data not from
agrovata containing anomalous data.
* ZEROED: initialised some variables to stop IOT trap failure.
* Handling of `missing' data in files added to:
abscale, absurd, agrovata, almn, amore, ecalc, f2mtz, fft, fftbig, fhscal,
freerflag, hklplot, icoefl, mtz2various, mtzdump, mtztona4, mtzutils,
na4tomtz, phistats, polarrfn, postref, rotaprep, reindex, rsearch, rstats,
scala, scaleit, sigmaa, sfall, sortmtz, tffc, truncate, unique, uudupl,
wilson.
* New programs:
* CROSSEC: Interpolate cross sections and compute anomalous scattering
factors (thanks to Don Cromer).
* GEOMCALC: Geomtery calculations on molecule (some overlap with `angles')
* HGEN: Generates hydrogen atoms for a protein coordinate file with standard
geometry.
* MAPROT: Map skewing, interpolating, rotating and averaging program.
* MTZMNF: Attempts to identify missing data in an MTZ file, and replaces
the entry with a Missing Number Flag (e.g. NaN).
* REFMAC: Garib's Maximum Likelihood refinement program. Brand new from York.
* RESTRAIN, TLSANL: `restrain' does constrained anisotropic thermal
parameter refinement using the translation/libration/screw-rotation model.
Its feature list says: refinement with restrained geometry, rigid body,
use of amplitude and phase observations, group anisotropic displacement
parameters, disordered solvent corrections (thanks to Birkbeck group).
`tlsanl' provides TLS analysis. Note restrain's keyword input isn't
in the standard CCP4 form.
* SOLOMON: density modification (phase improvement) by solvent flipping.
* SORTWATER: Replaces `watersort'.
* xdlmapman, xdldataman: have been added thanks to Gerard K.
* Library:
* library.nw removed after too many complaints -- source is now library.c
* lib/data/atomsf.lib has comment section added; some programs which read it
altered as a consequence.
* lib/data/crossec.lib: Data file for `crossec'.
* CCPOPN uses /dev/null and NL: interchangeably
* Fatal errors on diskio files now report the filename in question.
* Packed image routines (for mosflm, ipdisp): New version.
* MODLIB: MINV has been renamed to MINV3. A new routine has been added to
calculate the inverses of nth order matrices MINVN.
* MTZLIB: Facilities for dealing with missing data items. [Null attributes
for relational tuples? -- surely not!] Writing files with this facility
should probably not be done since the programs aren't guaranteed to
swallow the results.
* PARSER: Backslash is now a continuation character like `&' and `-'.
* RESTRAIN dictionaries: chiral_pep4.dic dna.dic nochiral_pep5.dic
chiral_pep5.dic nochiral_pep4.dic
* RWBROOK: Add deuterium to atom list.
* SYMLIB: new routine HKLRANGE.
* symop.lib: correct groups 120, 166, 210, 219, 220, 227, 228. File now
subjected to the overdue check for fulfilling group conditions on the
operators.
* x-windows/XCCPJIFFY/XCCPJiffy: colours changed to be consistant with those
defined in NPO. Also, Xloggraph and xplot84driver pen colours are the same.
* Altered write statements so they do not exceed vms write limit of 132
characters.
* Examples:
* All examples updated, inline with current progs.
* Runnable: crossec.sh, fractional-orthogonal, restrain,
unique-free-R (using new $CETC/uniqueify script)
* Non-runnable: restrain.exam, mlphare-MAD modified
* VMS: tracer.com, surface-volume-calc.com
* Documentation:
* FAQ: the plain text version with searching scripts (ccp4faq) are avialable.
Just type 'ccp4faq'.
* MLPHARE: more information about using MAD data.
* Out-of-date manual-usletter.ps removed -- the current one should print OK
on letter paper anyhow.
* Updates to mtzlib, npo, sfall, sigmaa documentation and the ccp4.1 man
page.
* Withdrawal:
* COMPLETE removed, see unique.doc for replacement procedure.
* FAQ in $CCP4 removed. It will be added to FAQ on the Web.
* ENVELOPE, FLATMAP, RESLICE, PRMAP moved unsupported status.
* LCF2MTZ, EXCHANGE and LCFLIB removed in the hope that everyone's using MTZ
files -- still available from Daresbury if anyone is in need.
* PLUTO removed, should now use NPO.
* WATERSORT was broken, replaced by `sortwater'.
Summary of significant changes to CCP4 at version 2.15
------------------------------------------------------
* Building etc.:
* configure tries to avoid messing with the `unsupported' directory if it's
not present.
* HPUX: don't set (invalid) amore (non-)optimisation flags. The correct one
reported to be needed, though.
* include/ccp4.setup-dist: Incorrectly (for any system) set _RLD_LIST,
causing chaos with dynamic loading on Irix and similar systems.
* MAKEFILE.COM: can now compile just one designated program with no checks.
* Fix problems building procheck on VMS.
* Program changes:
* CAD: Allow longer LABIN/LABOUT lines. Accept LABIN FILE <i> ALL.
* CONTACT: The output has changed to: Res type, Res ID, Atom name.
* IPDISP: Support MacScience scanner.
* MAPMASK: Symmetry expansion speeded up. New SIGMA option for SCALE
(useful when contouring).
* MTZUTILS: Fix zeroed columns from hklin2 for reflexions not in hklin1 with
UNIQUE option.
* NCSMASK: A crude `sphere mask' can be constructed by making a PDB file
with only a few atoms and specifying a large radius. Output map grid was
always 3A round coordinates -- now 2A+<rad>.
* PEAKMAX: symmetry related peaks at the edge of the map are not output.
* Library:
* QNAN from the diskio routines (almost unused) changed from a function to a
subroutine to avoid lossage with f2c's calling conventions.
* protin.dic: Last block wasn't read. WAT residue changed to contain more
extensive list of waters (oxygen) only. All other atoms (ZN1,CU) have been
removed.
* symop.lib: Errors corrected in SGs 43, 112, 115, 160, 210, 228, 230 (a
subset of errors reported with the X-PLOR version...)
* Examples:
* Remove unnecessary test_brk.brk
* Documentation:
* Several .doc files corresponding to man .1 files were missing. diskio.doc
was out-of-date.
* Various fixes/updates to documents for amore, ccplib, contact,
libsymmetry, lsqkab, ncsmask
* Withdrawl:
The programs scheduled for withdrawl aren't taken out of this realease,
which is mainly to fix bugs.
Summary of significant changes to CCP4 at version 2.14
------------------------------------------------------
* Building:
* XCCPJIFFY: Fix problems on Convex (but see comments in Imakefile).
* x-windows/README: The note about patches for xdl_view was obsolete.
* HPUX: Get the right version of the date routine under HPUX9. Attempt to
cope with `Convex' variant (gosh).
* Linux (and other) compilation with f2c: now assumes use of the `fort77'
script (untested on Linux so far)
* Program changes:
* AMORE: tidy up keyworded input: some dubious input which previously worked
may now be rejected.
* CAD: errors in keywords are now trapped better.
* DERIV: fixed bug in atom input
* DM: multitudinous ways to enter averaging matrices; skeletonisation
facility; output solvent masks could be ragbled in some SGs
* ECALC: More tables and xloggraph markup.
* FFT: grid sampling for P31(144) is now Nx=Ny=6n Nz=6n, for P21212a(1018)
Ny=4n Nz=2n and for P61(169) Nx=Ny=6n Nz=12n.
* HKLVIEW: reciprocal lattice spacing value in the output area was always
zero during a "measure"; rationalization of maximum resolution handling;
-rawname option.
* MAMA2CCP4: Allow Uppsala compressed format (re. O FAQ Q.731).
* MTZUTILS: Error is produced when two output columns are the same when
using INCL/EXCL. Problem with potentially using random resolution limits
fixed. Now defaults to ONEFILE if HKLIN2 not assigned and also checks for
HKLIN; per old documentation but wasn't implemented previously. UNIQUE
option failed when there were more reflections in hklin2 than in hklin1.
* NPO: RESIDUE EXCL now works as it should. Plus documenation more in
line with program. DCELL now works and map axes labels are always plotted.
Open scratch file in the scratch area.
* PDBSET: new options SYMGEN NCS, SELECT OCCUPANCY; fixed bugs in RENUMBER
input and in reading O datablock; new options BFACTOR MAXIMUM|RANGE,
SELECT BFACTOR, COM, REPLACE ATOM. O data blocks can now have comments and
case insensitive to data block type i.e. R
* PEAKMAX: Output overflow is now fixed.
* POLARRFN: ticks at 0, 90, 180, -90 are now sensible.
* PROCHECK: Version 3.3 (less the NMR stuff). See $CPROG/procheck/README
(no new manual). New script procheck_comp for comparing related
structures (also proplot_comp), both untested.
* PROTIN: Deal with multiplanar groups automatically. Re-dimension to cope
with current default dictionary. VDW contact checks weren't being done
between different chains in the same molecule. More consistency of error
messages so they can be found in the output.
* ROTAPREP: With RAXISDUMP (& WEIS) input only: for MPART>1, IPR would have
a garbage value. For SCALEPACK input: initial records shouldn't be read
as reflexions; strong reflexions were being read wrongly, effectively
divided by 10 because of inconsistent formatting by scalepack.
* RSEARCH: Does dynamic memory allocation.
* RWCONTENTS: Don't write to unconnected unit.
* SCALA: wrong values to be output in the modified SD columns SIGIC,
SIGIPRC, iff the input file contained a SCALE column (ie if the output
file from Scala had been run into the input for further scaling); fix
wrong reflection counts and array overflow with FINAL FULL.
* SFALL: The documentation and some output messages have been amended to
clarify confusion about the setting of nonstandard atom/residue types to
ZZZ/DUM. Some messages are now only output with VERBOSE. PG name could
get corrupted, confusing dm. For P4i2i2 SGs, phase was wrong for centric
reflexions h 0 l with h+l divisible by 3. Now checks for reflexions in an
incompatible AU for the SFSG requested. P3-specific SF and refinement
routines added.
* SIGMAA: map coefficients for PARTIAL and COMBINE changed, new labels --
see doc. Two sets of experimental phases can now be merged (with or
without HL). COMBINE syntax changed. Phase analysis transferred to
PHISTATS.
* UNIQUE: DEAFULT keyword for dummy column contents.
* WATPEAK: bad subroutine call could cause crash. Error fixed in calculation
of symmetry equivalents. Error in output fixed. Dmin default is now 0.1
and output expanded.
* Library:
* KEYPARSE: New module providing a higher-level interface for decoding
keyworded input.
* lib/data/protin.dic: Residue flags corrected per protin change. Fix to
avoid fatal error in protin.
* lib/data/protin_jp.idl: Format error for group DFP causing problems even
when the group not used.
* lib/data/symop.lib: typo in 72th symmetry element of F432 (209).
* MTZLIB,SYMLIB: SYMFR{2,3} no longer reset the start column to 0 and check
for a SYMM keyword there.
* PLOTSUBS: correct coordinate transformations used by PLTDBU, PLTMBU
* PARSER: The IDEC value returned by PARSE(R) was rubbish for integers and
not per doc for reals -- definition for integers rationalised (changed).
* RWBROOK: New routine RCELL to return cell parameters; remove the EJD
feature whereby atom types could be stored in columns 67-80 and clash with
footnotes. In RBROOK atom type ' W' is now Tungsten and not water.
* CCPOPN: Fix the Unix special case for /dev/null with CCP4_OPEN=UNKNOWN.
* New Programs:
* BONES2PDB: Convert BONES output to pdb file.
* MAPMASK: General map and mask manipulation program; can replace `extend',
`envelope', `prmap'.
* NCSMASK: Performs operations on non-crystallographic symmetry masks,
e.g. as a precursor to DM.
* PHISTATS: Phase analysis (the ANALYSE part of the old SIGMAA). NB. It is
probably more informative to do map correlation.
* POLYPOSE: A program for superimposing many multi-domained structures.
Written by R. Diamond.
* PROCHECK scripts, programs: procheck_comp, proplot_comp, mplot, rmsdev
(see above).
* STEREO: To reconstruct 3D coordinates from measurements of stereo diagrams
(from Michael Rossmann).
* Examples:
* For new programs: polypose, stereo
* RF-with-Es, toxd-RF-Es: rotation function with Es
* auto-amore, MR-with-amore: automated running of amore for a simple case
(unrealsitic toxd example removed)
* non-runnable/mapcutting: Prepare P1 map to calculate "model" structure
factors for molecular replacement.
* procheck/procheck_comp: there are VMS examples, although they both can be
run interactively.
* watpeak: Using toxd without the waters as the model. Then generating "new"
waters from an fo-fc map. These new waters can be compared with the
refined ones.
* Documentation:
* (Still insufficient) update of the print{ed,able} manual. It's possible
the description of the distribution in the printed one doesn't quite match
what's here.
* An FAQ is available, for what it's worth.
* Notice of withdrawal:
In the next release PLUTO will be withdrawn in favour of NPO and ROTAVATA
will be withdrawn in favour of SCALA. Also possibly/probably for the chop
as the functionality is elsewhere: extend, reslice, prmap, envelope,
flatmap.
Summary of significant changes to CCP4 at version 2.13
------------------------------------------------------
* Building:
* Configuration/installation was wrong for dynamic shared library
* Building mosflm-stuff failed if not building a shared library
* Library:
* CCPALC: now zeroes the memory chunk -- affects amore, at least
* protin.dic: New values for protein residues to improve bond angles.
Another co-factor has been added.
* protin_jp.doc: Gives an explanation of how JP dictionary was made. The
default dictionary is based on this.
* SunOS: CCPFYP now sets up abort for common floating point exceptions
* symop.lib: added spacegroup 1003 (P2 with dyad along Z)
* Program changes:
* ALMN: Now reads columns from HKLIN2 correctly.
* AMORE: SIGF is now compulsory. Crashes and garbage output due to
uninitialised data avoided.
* CONTACT: dimension increased.
* FFT{BIG}: Abcoeffs are now written out correctly.
* NPO: LABEL TEXT wasn't working
* TRACER: input now keyworded and input/output is now to standard
input/output rather than files; avoid crashes on some systems due to
unsaved variables
* WATPEAK: (omitted from 2.12 changes note): SYMMETRY is compulsory because
symmetry related waters are removed.
* Examples:
* Added runnable example for tracer
* waterpeaks now consistent with `watpeak' changes
Summary of significant changes to CCP4 at version 2.12
------------------------------------------------------
* Building:
* F2C compilation: be conservative about ability to unlink scratch files
(not actually done in 2.11)
* VMS: for DEC fortran remove /noopt in library build and use
/assume=(dummy_aliases) for programs to avoid possible problems with known
illegalities
* A dynamic shared version of the library can be built and installed on
Irix[56] and SunOS5 using the --with-shared-lib option to configure
* Library:
* XDL_VIEW: don't grab inappropriate events with popup
* Program changes:
* ABSURD: allow it ro read antique data
* AGROVATA: fix at 2.11 caused problems with anomalous data
* AMORE: avoid singular matrix from peaksearch on degenerate ridges
* FHSCAL: fix calculation of pseudo cell volume for vecref with multiple
derivatives
* MTZUTILS: didn't find HHL reflections correctly
* NPO: SIG and MAX sub-keywords of CONTRS has been added. Can now contour on
sigma levels or as fraction of the maximum (Atsushi Nakagawa). MAP 3D
option is now reinstated. SYMMETRY input got translation wrong
* PEAKMAX: ensure highest symmetry-related peak not rejected
* PROLSQ: NOUPDATE option expurgated from code and example in doc
* PROTIN: dimensions increased
* REINDEX: avoid /0 etc. problems with null orientation block in input
* ROTAPREP: pick up SIGF column if LABIN not used; abend if no reflexions
passed etc.
* WATPEAK: now has dmin cutoff and will check for symmetry related peaks
to accepted waters.
Summary of significant changes to CCP4 at version 2.11
------------------------------------------------------
* Building:
* (Unix) binsort didn't get compiled/installed
* IRIX64: 6 is recognised by configure with target `irix' (but we have bad
reports about the 6.0 compiler)
* Irix5.2: avoid X installation misfeature (files installed owned by root)
* F2C compilation: be conservative aboutability to unlink scratch files
* Library:
* XDL_VIEW: bug fixes which probably don't affect ccp4 programs
* lib/data/protin.dic RNA residues have been improved + other changes.
* CCPLIB: correct off-by-one in month value from f2c and AIX IDATE (showing
up in the banner); avoid dates sometimes coming out in US order
* Program changes:
* AGROVATA: numerical problem in rejection in some circumstances; use scala
SIGIC, SIGIPRC columns
* COORDCONV: changes for CSD format at v2.3 were bogus
* CONTACT: translational parts of SYMMTERY were ignored; could fail due to
undefined variables
* HKLVIEW, IPDISP: avoid crash in some circumstances
* MTZ2VARIOUS XPlor output for anomalous data is now correct. Also, DP
sigma cutoff has now been removed.
* NPO the LIMIT keyword works and has been reinstalled.
* OVERLAPMAP: now gives total correlation for main chains and side chains
seperately
* ROTAPREP: check BATCH specification properly and make code easier for
adding new input types
* RSTATS: preserve SIGFC and FREE in output with OUTPUT FOFC
* SCALA: problems with optional columns (manifest with Denzo output, at
least) fixed; Omit "too strong" reflections from initial scaling; New
output columns SIGIC[, SIGIPRC], corrected sd(I), sd(IPR)
* SFALL: potential crashes from unsaved variables
* VECTORS: avoid crashes from coding error
* New programs:
* RFCORR: Analyis of correlations between cross- and self-Rotation functions
* Examples:
* Added runnable examples for: agrovata, rotavata, scala, truncate
* Fixed: tffc_procedure, icoefl
Summary of significant changes to CCP4 at version 2.10
------------------------------------------------------
* Citation: The appropriate reference for citing usage of the suite is now
Collaborative Computational Project, Number 4. 1994. ``The CCP4 Suite:
Programs for Protein Crystallography''. Acta Cryst. D50, 760--763.
* Building:
* IRIX5.2: [introduced un-noted at 2.8] configure attempts to solve problems
with rewinding scratch files a la 5.1
* rsps compilation ignored the setting of `FC' -- wrong for HPUX, at least
* ipdisp should now build and run under VMS
* `iris3000' configuration removed to avoid confusion with R3000-based Iris
systems -- no evidence it ever worked anyhow
* psaver wouldn't compile e.g. on convex
* AIX: wrong `install' program was used
* VMS: fix makefile.coms for xdl_view, hklview, rsps, creation dates compared
* F2C can be used to compile the suite. This may be of interest to those
who'd otherwise need to buy a compiler. It's adequately fast with gcc.
Use configure flag --with-f2c (unless on linux or freebsd).
* Linux and FreeBSD configurations are available (untested) using f2c
* The `binsort' program has been moved from lib/src to src.
* XDL_VIEW library updated to a newer version that doesn't need patches for
OSF; hklview, ipdisp now use it
* Titan: fixes made but untested
* Library:
* CCPLIB: CCPERR now prints the program name so you can easily see what
failed at the tail of the log file; it should also print error messages on
the unix standard error stream; CCPPNM is a new routine to return the
program name. CCPALC etc. can now cope with 12 arrays, including
LOGICAL*1 (deprecated). CCPOPN messages can now be suppressed using -v as
for QOPEN ones and don't cause write errors with long path names.
* MAPLIB: changed format of mean & RMS density print (Uppsala request); this
might break awk-ward things that look for this information in the old
format-- sorry
* MTZLIB: Change dimensions (and parameterise) to allow 192 symops, not 96.
(3 non-protein groups in symop.lib have this many operators.) LWHSTL is a
new simple interface to LWHIST for writing standard history records. The
mtzlib object size is somewhat smaller. Avoid problems with clashes
between program column labels and file labels when the columns aren't
actually the same. LOOKUP now initialised as -1 compulsory, 1 soft
compulsory (for agrovata/rotavata etc.) and 0 optional. Other programs
have also been affected.
* pack_c.c: add AIX, HPUX calling conventions
* PARSER: various long-standing lossage in PARSE and PARSER corrected,
especially handling of comments and continuations; now works as documented
in ccp4.1 and the manual, I think. Documentation somewhat improved.
* RWATOM: deleted -- Dimaond format no longer supported by any programs
* SYMLIB: Change dimensions a la MTZLIB; EPSLN now general; some changes to
point group name handling in PGNLAU for consistency with Int Tab.; P61/P65
now NZ=12n.
* symop.lib: typo in SG166
* MAPLIB: Change dimensions a la MTZLIB
* scatcoef.lib obsoleted by changes to vecref
* PLOTSUBS: add routines moved out of polarrfn
* lib/data/hist.lib: added for dm
* lib/data/protin.dic: replaced by John Priestle's, based on Engh/Huber
parameters with York cofactors added.
* lib/data/protin_vl.idl: alternative protin dictionary from Victor Lamzin
(see lib/data/protin_vl.doc)
* BINSORT: programs that do sorting now should always abort (ungracefully)
on disc full errors etc. rather than reporting zero records returned from
the sort and continuing.
* Program changes:
* AGROVATA: partials weren't handled correctly for non-mosflm data; avoid
the need for SCALE with 1 batch; fix array bound errors with all batch
nos. 1
* AMORE: TABFUN accepts NOSHIFT or NOTRAN equivalently; fix failure of
TABLING on some systems due to not closing scratch files; error in
calculation of RF standard deviations; errors in treatment of Miller
indices (which could cause spurious failures) corrected but means that
previously-generated HKLPCK and TABLE files need to be regenerated; TRAFUN
failed in polar space group
* AREAIMOL: potential problems due to uninitialised variables; check for
atomic number written at the end of a PDB line for cases of nonstandard
atom naming, like sfall.
* BAVERAGE: changes to output
* CAD: RESOLUTION OVERALL wasn't obeyed
* EXTEND: proper action if symmetry mangled: if SG number <= 1, set to P1,
else bomb with message; make check against asymmetric unit volume a
warning, so that it can work in projection
* FFT: Grid in P61/P65 must now be NZ=12n.
* FHSCAL: can scale up to 20 datasets; BIAS now defaults to 0 (assuming the
worst of the data processing program).
* FREERFLAG, MLPHARE, REINDEX, SFALL, SIGMAA: add history to HKLOUT
* HKLVIEW: draws labelled axes
* IPDISP: correct calculated resolution of outer circle. Async I/O removed
to work on OpenVMS. Dialogue box no longer locks screen.
* MAPSIG: keyworded; could loop on default input due to uninitialised
variable
* MLPHARE: Parameters reset properly HLA .. HLD and FHn, FHAn are now
correct on output. LABOUT ALLIN works + program checks to see if input
column labels are the same as program labels.
* MTZ2VARIOUS: TNT output option and EXCLUDE FREER option; USER output
option; SHELX output flagged for free R if appropriate
* MTZDUMP: include zero values of type H, P or A in the resolution
statistics
* NPO: LABEL FIX atom_name and LABEL atom_name now work properly. LABEL
atom_name was not accually possible before. Also input cards echoed in
output.
* OVERLAPMAP: PATTERSON option (a la GROPAT)
* PDBSET: REORTHOGONALIZE and REPLACE RESIDUE options
* PEAKMAX: symmetry-related peaks not output
* PLTDEV: fixes to scaling for PostScript output
* PRMAP: end-of-file on input now just prints map header
* PROCHECK: version 3.0.1 as released by Roman Laskowski, but with some
programming errors fixed and using CCP4 file opening routines. Includes
colour plots etc. New manual in $CDOC/procheck.doc and
$CCP4/manual/procheck/manual.ps. Note the accompanying licence in
$CPROG/procheck/confid.doc
* PROTIN: default dictionary improved (see above)
* ROTAPREP: reading XDS files and F+, F-, sigmas are now root(2)*SIGIMEAN.
* ROTAVATA: didn't accept MAXWIDTH keyword to pass to agrovata; fail
gracefully when zero reflexions accepted in a batch
* ROTMAT: wouldn't run without complaining about missing CRYSTAL; slight
additions to output
* RWCONTENTS: count of hydrogens was wrong
* SCALA: Made phi range errors warnings up to maximum of 50 errors; SKIP
option; OUTPUT OMIT PARTIALS option: Don't keep partials if not being used
for scaling (should speed things up)
* SCALEIT: now defaults to NOWT option (ignore SDs of data); new keyword
WEIGHT to use SDs.
* SFALL: Improve some error messages; SFSG now defaults to an appropriate
value (highest symmetry consistent with the data) so you don't have to
look one up. Grid in P61/P65 now NZ=12n. LABOUT ALLIN works + program
checks if input column labels are the same as program labels. Using
FPART PHIPART was broken.
* SIGMAA: new option to set resolution limits for phase combination
("COMBINE LOW|RESOLUTION")
* TFFC: allow much longer buffer for entering input label assignments which
may be needed in some cases
* VECREF: new keywords RCUT, DAMP; use atomsf.lib scattering factors rather
than scatcoef.lib; improved treatment of large Bs; sites with low
occupancy or silly B factors not output; allow negative occupancies; THRE
& BLIM options; dynamic memory allocation.
* WILSON: END keyword; coding error caused failure sometimes
* New programs:
* DM: all-singing, all-dancing density modification: solvent flattening in
one program, histogram mapping, Sayre's equation, molecular replacement...
See also the document doc/dm_ncs_averaging.doc
* MAMA2CCP4: convert Uppsala-format masks from MAMA to CCP4 format (`mapman'
isn't currently correct on this)
* RESLICE: A simple-minded resectioning program; interchanges axes in core
("unsupported")
* STNET: Generate stereographic net plot for use with polarrfn
("unsupported")
* General:
* History records written to HKLOUT now mostly have date and time included
to give a better chance of figuring out sequences if necessary.
* Keyworded input may give less unpleasant surprises now due to fixing of
`parser'
* Vestiges of Diamond format coordinate files removed
* Examples:
* Original toxd dataset had wrong column type for ANAU20
* examples/vms is now much fuller
* Updated or added examples in examples/unix/runnable: mir_steps, vecref.sh,
scaleit.sh, patterson (replaces fft.sh), dm.sh, 3fofcmap, f2mtz.sh &
mtz2various.sh (using free R and X-PLOR type), rsps.sh, fhscal.sh,
polarrfn.sh, scaleit.sh, mtzutils.sh, npo.sh
* Manual:
* Minor changes to the text -- no new printed version currently.
* To format the LaTeX for US letter paper (rather than A4) uncomment
`\letterpapertrue' at the top of manual.tex and run `dvips' appropriately.
The result is now available as manual-usletter.ps.
Summary of significant changes to CCP4 at version 2.9
-----------------------------------------------------
* VMS: reading MTZ files basically didn't work from v2.7 -- records were
essentially all zeroed under most circumstances
Summary of significant changes to CCP4 at version 2.8
-----------------------------------------------------
* Building:
* PSAVER wouldn't build under DEC Fortran (broken at 2.7, sigh)
* VMSDISKIO compiled with some fortran versions, despite containing junk,
but not with others
* Library:
* PARSER: avoid problems with @-included files which, e.g. caused `unknown
keyword' problems with @-files of solutions read back into amore
* SYMOP.LIB: 2 typpos: `_' for `-'
* Program changes:
* MLPHARE: Bug for MAD data: it assumed it could estimate the centric phase
from the the first FH, which doesn't work if your first FH = 0.0.
* SFALL: UnSAVEd variables could cause failure sometimes
Summary of significant changes to Csignificant changes to CCP4 at version 2.7
-----------------------------------------------------
* Building:
* HPUX: Enable some floating point traps in OS v9 and remove abort on all
other signals
* The `ranlib' step was omitted after the mosflm-stuff target in the
library; affects BSD-like unixes
* VMS: The MAKEFILE.COMs would only work with DEC Fortran (OpenVMS) (?)
through using a .F extension
* Library:
* IRIX 5.1: enable rewinding of scratch files (at the expense of them not
being deleted if the program crashes); there may be other problems with
irix5.1
* IPDISP: changes for building in VMS (yet untested)
* MAPLIB: MSYCPY mangled the symmetry information if maps were transported
between machines with different byte orders; affects programs extend,
overlapmap, mapreplace, zeroed
* MTZLIB: speed up reading and writing MTZ files somewhat by avoiding a
subroutine call for each datum
* VMSDISKIO: efficiency improvements and QINQ now works (but never used?)
* XDL_VIEW: typo prevented compilation; Makefile altered; (untested) VMS
MAKEFILE.COM
* Program changes:
* AGROVATA: removed VAXtran; BINS RECIPROCAL option allows binning by equal
volumes in reciprocal space
* BAVERAGE: code polished
* COORDCONV: fix possible uninitialised variable; maybe speed up reading of
X-PLOR format
* FFT{BIG}: coding error caused core dumps in some cases
* MLPHARE: increase maximum refinement cycles
* MTZUTILS: resolution restriction didn't always work with two files
* PEAKMAX: The incorrect peak height (NEXT peak in the sorted list rather
than current) was being written to the output Brookhaven file in the
"occupancy" column.
* PROLSQ: VDW contacts not used properly; fixes to allow variable
non-crystallographic symmetry
* PROTIN: fixes to allow variable non-crystallographic symmetry; increase
maximum number of atoms
* ROTAVATA: BINS RECIPROCAL allowed in line with agrovata
* ROTMAT: insist on CRYSTAL input
* SCALA: bugs affecting INTENSITIES PARTIALS option
* SFALL: source code re-vamped; error with ALLIN and >29 columns; problem
with error estimate could cause failure; removed SAVEs to give
optimisation a better chance.
* SIGMMA: phase analysis instrumented for xloggraph
* VECTORS: allow atom lines to have extra fields on end
* WATPEAK: two new totals; dimensions increased
* Documentation changes:
* FFT: correct some SG-dependent info
* FHSCAL, VECREF: minor changes
* ROTMAT: more explanation/clarification
Summary of significant changes to CCP4 at version 2.6
-----------------------------------------------------
* Building:
* SYMLIB: non-standard fortran
* OSF/1: unaligned access wasn't fixed
Summary of significant changes to CCP4 at version 2.5
-----------------------------------------------------
* Building:
* Typpos caused failure on: ESV (/Titan?), VMS
* OSF/1: `make' infelicity caused failure; OSF check missing from chelp
(mosflm bits only); OSF `fsplit' failed on rwbrook.f, symlib.f; mtzlib
caused unaligned access errors on OSF/1 (generally wrong for 8-byte C
longs)
The xdl_view-based code won't work asis (due to 64-bit pointers).
`x-windows/osf-patches' supplies patches specific to OSF/1 pending a new
version of xdl_view.
* AIX: amore optimisation flag wrong
* VMS MAKEFILE.COMs now try to reset working directory sensibly
* SCALA directory needed re-naming for make to work
* MSTAMP omitted from makefile
* RSPS sometimes printed symmetry operators wrong
* ccp4.setup-dist had a typo in the XUSERFILESEARCHPATH definition
* Library:
* Dynamic memory allocation was wrong for integer arrays -- they only got
half as much as they should have done. Might have affected amore results.
* CCPLIB: add CCPNUN for finding unconnected i/o unit.
* QSEEK errors now hint that the file may be corrupt.
* PARSER: avoid echoing lines when reading `@'-file e.g. symmetry headers
from agrovata
* SYMLIB: SYMTRN was wrong for operators n/4
* Program changes:
* AMORE: improve error messages
* HKLVIEW: can display columns other than of type F or J (eg W)
* IPDISP: minor changes and new detector types
* MLPHARE: minor corrections - aniso eigen vectors not printed
* PLTDEV: fix picture range selection
* SCALA: cope properly (?) with absent orientation blocks; if scaling with
fullys only, skip reflections with le. 1 full (this speeds things up a lot
in many cases); doc change
* SFALL: didn't cope with an MTZ file with RESO 0
* XCCPJIFFY: changes for OSF/1 had been omitted
Summary of significant changes to CCP4 at version 2.4
-----------------------------------------------------
* Building:
* library.c wouldn't compile with Sun bundled compiler and probably other
K&R ones
* amore optimisation flag was invalid on Sun with SunPro compiler (at least)
* rsps compilation flags changed for Irix to try to avoid v. long
compilation and reported compiler crashes
* Library:
* SYMLIB: PG 321 was written out with the `PG' missing
* PARSER: bug with lines exactly 133 characters long
* Program changes:
* AGROVATA: fix in absence of MPART column
* AMORE: rotfun could output garbage; dimension was set incorrectly for
sorting step
* BAVERAGE: error in xloggraph output
* DISTANG: change error report
* ECALC: coding error with PG name
* FFT: wasn't removing scratch file (at least in VMS)
* GENSYM: can now generate more than one cell
* MLPHARE: can now use 20 derivatives
* MTZ2VARIOUS: read Is ready for SHELX
* NPO: bugs in GRID command
* PDBSET: add ELEMENT option; typo could cause bad error message
* POLARRFN: small error in calculation of mean & rms
* RSPS: attempt to remove illegal code had broken the command loop --
current version may not compile (correctly)
* ROTAPREP: fix batch number for XDSUNIQUE, TEXHKL, MUI, MUF; generalise (?)
DENZO
* RSTATS: error for PROCESS FOBC (width multiplied by scale factor for every
reflection)
* SCALA: flow.h and refflg.h were missing; make XDET, YDET, ROT columns
optional if not used
* SCALEIT: can now use 20 derivatives
* TFFC: coding error with PG name
Summary of significant changes to CCP4 at version 2.3
-----------------------------------------------------
* Administrivia: CCP4 is now funded by the Biotechnology and Biological
Sciences Research Council following the demise of SERC. Note also the new
FAX number for CCP4 if you need it.
* Change policy to avoid the distinction between major and minor released
versions: too much work and scope for mistakes.
* Most Fortran files now .f rather than .for as required ages ago by the
Working Group: more convenient on un*x and no problem on VMS.
* VMS library: C code replaced by (faster) VMS-specific Fortran
(vmsdiskio.for), avoiding an apparently insurmountable RTL library bug. The
script MOSFLMBITS.COM an be used to build the extra library modules for
MOSFLM if required.
* Free R factor facilities: programs affected (only additions): freerflag,
sfall, fft, mtz2various, f2mtz, rstats. Note the opposite convention to
X-PLOR -- free R flag is a weight (but not yet used as such). The
conventional way to arrange calculation of the free R from an mtz file is by
using `LABIN FREE=FreeR_flag'. See individual program documentation and
some altered examples.
* Manual and examples: various fairly minor updates.
* Library:
* changes on termination: try to give helpful system error message and not a
misleading one, fix problems with EXIT on AIX, HP-UX and ISATTY on AIX;
* Some scratch files weren't being deleted under Irix. They should now
vanish, possibly unless the program crashes.
* [ccplib] CCPALC, CCPALE, CCPE2I: facility for dynamic memory allocation
(mainly for amore so far); correct handling of `-d' command-line flag.
* [diskio] MSYWRT: added; properly-typed variants of QREAD/QWRITE: QREADR
etc.;
* [modlib] RANMAR, RMARIN: random number routines added
* `magic number' code for absent data flags was completely bogus, fortunately
not used;
* add CCPMVR, CCPZR, CCPCPI;
* SYMLIB: avoid possibly echoing symop file due to undefined variable;
changes in step with symop.lib PG changes; remove 80-character limit on
SYMMETRY input.
* PLOT84LIB: tidying up and removal of undefined variables
* Fix problems with read/write diskio files on SunOS, ESV, Titan, at least.
* lib/data/symop.lib now has all standard SGs (and some non-standard) and
correct PG names; symop_all.lib removed.
* lib/data/protin.dic: format error in the planar restraints of the NACETYL
group
* lib/data/VLdict.dic was bogus -- removed. The default protin dictionary
is what this was supposed to be.
* Installation:
* Titan may now work;
* VMS .com files changed, especially for `make'-like facility in
CPROG:MAKEFILE.COM to avoid re-building up-to-date programs; now don't
need a C compiler for the basic library (as above);
* New programs:
* REBATCH: alter batch numbers in an unmerged MTZ file (saves running Mosflm
again); beware -- not well tested.
* FREERFLAG: tags each reflection in an MTZ file with a flag;
* MSTAMP: add machine stamp to MTZ or map files lacking it (unsupported);
* PSAVER: partial symmetry averaging;
* SCALA: scale together multiple observations of reflections (rotavata
replacement, previously aggregated);
* SYMFIT: fit best molecular transformations to sets of coordinates related
by non-crystallographic symmetry (unsupported).
* X-WINDOWS THINGS: the XLOGGRAPH, XPLOT84DRIVER, IPDISP and HKLVIEW
programs are now considered part of CCP4 (previously aggregated). The
sources live in $CCP4/x-windows. They aren't built and installed with the
rest of the programs. Modify the makefiles in the individual directories.
* Withdrawn:
* HEAVY: use mlphare;
* POLSIG: unnecessary with current polarrfn.
* Program changes:
* ACT: wouldn't run in many cases;
* AMORE: dynamic memory allocation -- can change dimensions without
recompilation (but doesn't necessarily reduce the virtual memory needed);
small fixes; some Spanish translation!
* AGROVATA: Re-dimensioning. FSAFE option now works. Added WIDTH WILSON &
WIDTH SQUARE options for alternative binning on intensities. Change
binning of partial bias correction analysis to allow bias of +-20% rather
than +-10%. Significant changes to allow addition of partials spanning
more than 2 images, and to make use of the new column MPART containing the
partiality indicator output by MOSFLM. These changes are essential to
deal with data from MOSFLM version 5.20 or later versions. New keyword
MAXWIDTH specifies maximum allowed width (in images) for partials.
* BAVERAGE: correct format error
* CAD: default resolution to agree with documentation; got lattice type wrong
* COORDCONV: changes for SHELX and Cambridge database input; code tidied
* ENVELOPE, FLATMAP: Avoid use of logical*1 true/false in mode0 map -- can't
transport results between compilers.
* EXTEND: remove check on input map starting at grid point 0,0,0, also fixed
minor bug (which caused some unnecessary work in a few cases). Assumed
(incorrectly) that all asymmetric units were mapped from point (0,0,0).
* F2MTZ: `X' column type for X-PLOR free R fudge; correct format error in
example.
* FHSCAL: END keyword, runnable example.
* FFT{BIG}: defaults for Patterson SG were broken. SG47 was not actually
wrong if not defaulted, contrary to previous alarm. fftbig now does
dynamic memory allocation. HKLMAX option for anisotropic resolution
(strongly discouraged for normal use). Allow explicit symmetry operators
without bombing. Allow sensible input of multiple scales [Bfactors] from
the same line. Logic error for phase of reflexions with |Fph(calc)|=0 in
double difference maps.
* GENSYM: now writes out CRYST1 & SCALE lines to PDB file; new READ option;
ATOM lines can have extra fields.
* LSQKAB: dimensions increased
* MLPHARE: output tidied; redimensioning; all reflections written out even
if not phased; correct labels for 5th, 6th derivatives
* MTZ2VARIOUS: Free R flag added and o/p compatible with X-PLOR. For any
phase columns present must negate the phase when generating the Friedel
pair. This applies to solvent correction term and PHIB term. Option to
read columns DP, SIGDP, ISYM for anomalous differences, to write out hkl &
-h-k-l if Danom present. Avoid mangling indices sometimes. Didn't reject
reflections with SIG=0.0. EXCLUDE, FPMAX, FPHMAX, FSQUARED, SCALE
options. RESTRAIN o/p type.
* MTZTONA4/NA4TOMTZ: run-length encoding option; NaNs in the file handled
properly (for use with absent data when implemented elsewhere).
* MTZUTILS: SCALE option.
* NPO: avoid calling GETENV (bogus in VMS); fix for different contour
colours at some level
* OVERLAPMAP: ADD option
* PDBSET: UTOB option
* PLTDEV: not outputs conforming PostScript; default scaling still broken.
* POLARRFN: correct logical name COEFFS; NOPRINT option
* PROCHECK: coding corrections. Un-mangled procheck.doc. Note that there
is a newer version available from
ftp@bsmcha1.biochem.ucl.ac.uk:pub/procheck for which we don't have
distribution permission and which isn't for commercial use. v3.0.1 has
coding problems with undefined/unsaved variables for which you can get a
patch from us if these cause problems.
* PROTIN: check VDW contacts in first chain when only one chain present.;
re-dimensioned; default NCODE = 1 (only matters if you input CELL here);
check array bounds and report all errors in input at the end.
* ROTAPREP: reorganise code to make additions easier; update documentation,
especially lies about formats; fix bad batch numbers with DENZO input;
BATCH compulsory; SCALEPACK input only wrote the first I which broke
rotavata with INTENSITIES PROFILE
* ROTAVATA: avoid array bound errors and undefined variables.
* ROTMAT: corrections, particularly for Merlot NCODE.
* RSPS: updated version from Stefan Knight;
* RSTATS: partial re-write and add free R.; END keyword; avoid infinite loop
due to numerical problems
* SFALL: disallow both RMSSHIFT and STEPSIZE; free R factor; use NOSCAL if
map input; other alterations, especially for ARP use.
* TFFC: SPACEGROUP/SYMMETRY now optional.
* WATPEAK: would only read first chain; write coordinates of each peak to LP
output
Summary of significant changes to CCP4 at version 2.2.4
-------------------------------------------------------
* abscale: over-long format
* act: wouldn't run in many cases
* agrovata: avoid integer overflow
* cad: default resolution agrees with doc
* gensym: wasn't built by unix Makefiles
* mlphare: long-standing error in figure of merit table
* prolsq: wasn't listing bad distances
* rotaprep: wrong for TEXHKL; initialise some variables (e.g. gave bad batch
with denzo)
* rotavata: assumed static allocation
* rsps: bad format writing score table
* sfall: problem if SMIN = 0.0
* watpeak: would only read first chain
* examples/toxd/solflat-cyc: add NOSCALE in sfall
* lib/data/protin.dic: format error
* mtzlib: error in Groningen changes in LRREFF possibly causing
reference of unset variable; LWBTIT incorrect: affects rotaprep
output, in particular
* build on AXP VMS: problems with com files, C code; allow for vax number
format
* vms library: prints process time at end, not session
Summary of significant changes to CCP4 at version 2.2.3
-------------------------------------------------------
* scaleit: problems with xloggraph o/p
* almn: bad rms density calculation
* deriv: didn't open hklin
* mtzvarious: correct X-plor o/p
* library:
* problems with rewinding some scratch files on Convex, ESV; setting logical
NATIVEMTZ ignores file machine stamp in reported VMS case where files had
bad stamp
* problems with CCP4_OPEN hadn't been properly corretced at 2.1.1, sigh
* ESV: avoid configure lossage if /usr/ucb isn't on path (shouldn't it be?)
* examples: correct peakmax o/p in a couple of cases
* proclean: uninitialised variables corrected (probably doesn't matter)
* exchange: wouldn't write the LCF file (the only place it's allowed)
* mosflm bits (image packing) wouldn;t build on osf/1
Summary of significant changes to CCP4 at version 2.2.2
-------------------------------------------------------
* binsort building still failed (some unix only)
Summary of significant changes to CCP4 at version 2.2.1
-------------------------------------------------------
* configuration/building: error building rsps (unix) and procheck (VMS) and
binsort (some unixes). Other changes for Concentrix only.
* polarrfn: plotting error
* prolsq: check for BATOM set but not XYZB in sfall
* protin: long standing error affecting intra-chain special distances
* Library errors causing general problems:
* setting CCP4_OPEN other than to UNKNOWN was treated wrongly in some cases
* maplib: serious array bound error
* parser: failure to read E-format real numbers
* lib/data/symop_all.lib: corrected
* examples/unix/runnable/waterpeaks: previously omitted
[Note that polsig is actually obsoleted by changes to polarrfn.]
Summary of significant changes to CCP4 at version 2.2
-----------------------------------------------------
* Binary file transparency: the low-level i/o routines can now read MTZ and
map files written on architectures with different number formats *providing
they are written with this version of the library*. There is some overhead
in this, but no significant overhead reading files written on the same
architecture.
Note that not all the possible combinations have been tested...
* Categorisation of programs: There is a new `unsupported' category of
programs. (This does not imply that we guarantee support for the others.)
They are supplied asis and we will not necessarily fix them (but still
welcome bug reports or your fixes). Many obsolete programs have been thrown
out completely. You can install only the major programs and not the
unsupported category if you want. There is a new directory: `unsupported'.
* Documentation
* There is a much-expanded, but still incomplete new manual. This includes
material formerly in the `overview' man `page'.
* new directory man/man3 for library man pages (incomplete)
* There is now a document for every program (we hope) and many have been
much revised and improved. Complete formatted copies are supplied, along
with man `whatis' files and the .doc files can be used with the unix man
system. Most of the documents have been examined and revised.
* Examples: the examples/unix/runnable directory has scripts which will run
with the small dataset from examples/toxd (which also contains working
scripts). The `ctest' directory has been removed.
* VMS library support: the VMS assembler routines have been dropped -- we now
only provide the C version of the low-level library routines since we can't
maintain the assembly code.
*You need a C compiler for the VMS compilation now.* See the manual for how
to get the free GCC compiler if necessary (although this hasn't been tried
for building the suite).
The C routines are slower than the old assembler ones -- sorry. If this
proves to be a particular problem, let us know.
* Changes/fixes to configure and makefiles and VMS installation; the latter is
now simpler and cleaner but is not guaranteed in OpenVMS yet -- please let
us know.
* Library bug fixes
* mtzlib: IPRINT=4 didn't print symmetry any more; user label input and
output variables reset in lropen and lwopen
* some timing routines were wrong
* the setting of CCP4_OPEN is now obeyed for MTZ and map files
* BINSORT alignment problem on some architectures
* possible inability to redefine logical names in VMS
* General library updates
* MODLIB: routines removed: match, ma21ad, mc10ad
* MTZLIB: more batches allowed; interpret absence flags from the Groningen
BIOMOL system (just set to zero at present)
* SYMLIB: routines removed: turnip, turn3, decsym, syminv, iminv,
symat; added: patsgp; changes to symop.lib; more batches allowed; new
library data file symop_all.lib has all Int. Tab. A SGs
* FFTLIB: added routines factrz, fndsmp, setlim, setgrd
* GRAFLIB: no longer included by default. routines now in PLOTSUBS removed
* PLOTSUBS: replaced with routines removed from graflib
* removed modules: graphics, hlplib, mdflib, optfftlib, plot9x, lib_kraulis,
frodo_maplib, mthlib, hdrlib
* LCFLIB now won't *write* LCF files
* `ccperr' now tries to report the last system error and times in VMS
* PARSER: new routines RDRESL, GTTREA, GTTINT; the (mis)feature of allowing
arithmetic between values read by the parser has been removed
* MAPLIB: improved precision of RMS & mean calculation
* $CINCL/{default,environ}.def: tidying and commenting
* protin.dic: updated and an alternative provided (VLdict.idl) from
Victor Lamzin
* code for binary file transparency (as above)
* Lots of internal reorganisation
* Significant program bug fixes
* ABSURD: problems with `reindex'
* AGROVATA: xloggraph o/p wrong; default INTENSITIES is PROFILE; changes if
SCALE column present
* ALMN: divide-by-0 errors
* FFT: error for spacegroups P65 (and 61 ..); get Patterson SGs correct
* FHSCAL: several corrections
* HKLPLOT: spurious 'Disagreement between symmetry operators'; error in
multiplicity
* MLPHARE: fix divide-by-zero etc.
* MTZ2VARIOUS: don't output excluded reflexions, treat formats as similarly
as possible; output |FPH-FP| if FPH assigned; END not compulsory; output
always to HKLOUT
* OVERLAPMAP: fix problems of rounding errors in calc. of correlation coeff.
* POLARRFN: failed to calculate rms value; put weighted RMS & mean
into map header; correct sampling intervals in map header
* PROLSQ: can no longer attempt to access hkl{in,out} (lcf files)
* REINDEX: new version
* ROTAPREP: takes DENZO input and madnes for050 files
* ROTAVATA: confusion about FTWO/NOFTWO rejections between ROTAVATA and
AGROVATA; change default on number of batches
* SFALL: various small changes
* VECREF: made consistent with FHSCAL (errors in them cancelled out)
* WILSON: xloggraph plot
* Significant program updates
* ABSCALE: new REINDEX option; changes for mosflm summed partials
* ABSURD: storage increase
* AGROVATA: accepts SCALE column etc.; redimensioned; ROGUES file extended;
changes for mosflm summed partials; negative values of SDADD
* ALMN: peak search changed, restored weighting of RMS & mean
* CAD: fairly major re-write
* COMPLETE: changes for triclinic data etc.
* COORDCONV: was coord_conv
* ECALC
* EXTEND: new algorithm; MAPSYMMETRY option
* F2MTZ: CTYP obligatory; FORMAT option
* FFT, FFTBIG: EXCLUDE option; changes to default grid
* LCF2MTZ: grok multi-record lcf files
* MLPHARE: various
* MTZDUMP: now as previous `dumpreso'
* MTZUTILS: wasn't applying resolution cutoffs to output file
* OVERLAPMAP: CHAIN option; change residue packing
* PDBSET: various extra options
* PEAKMAX: keyworded and various other changes
* PROLSQ: new LIMIT keyword; various other changes
* ROTAVATA: default INTENSITIES is PROFILE; changes for mosflm summed
partials
* SFALL: various changes
* SURFACE
* TRUNCATE: changes to interpolation etc.
* WATPEAK: includes contact list; carries through occupancy, B-factor info.
[Changes to things in the `unsupported' directory not given here, although
many have had some changes.]
* New programs
* ACT: analyse coordinates.
* AMORE: monolithic molecular replacement program.
* GENSYM: symmetry-related sites from atoms and list of vectors within
defined volume
* NPO: new version of PLUTO
* PROCHECK system: stereochemistry checking
* RSPS: Patterson searching (previously aggregated)
* UNDUPL: essential for some data from Madnes (following Absurd).
* VOLUME: polyhedral volume around selected atoms
* Programs deleted or moved to the aggregated directories (with some
suggestions for alternatives):
accsa, area [use areaimol], atconv, atomsf, atpeak [use watpeak], bavsc2,
brk2dia, brkmat, brksort [use procheck], burgess, cadpro, chelp, chkplt,
cli_help, convrnxp, coordswap, crossec, dabs, deg, diffop, dumpreso [use
mtzdump], hlbgen, hlptree, limits [use pdbset or extend], mapbrick [frodo],
mapcont [frodo], mapform [use mapexchange], minlim [use extend/pdbset],
nadia [use angles/procheck], o2brk [O distribution (replaced by pdbset)],
oscgen [with mosflm], patvec [use vectors], pdbrot [with ribbon], pltout
[with ribbon], postplot [with ribbon], peaksearch [use peakmax], resection,
reslicer, ribbon [aggregated], ribrot [with ribbon], rwbred, skewbrk, splitd
[ribbon], symgen [use pdbset], tidytext, transz1, xplor2pdb [use pdbset],
xyzlim, xyz_modify [use coordconv]
* Housekeeping: (All?) the distributed files have been examined and only
relevant ones should now be distributed. All the programs should now print
version (date) information when they run.
* Binaries will normally not be supplied on VMS tapes now. (We can't make AXP
binaries anyway.)
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