-*- mode: indented-text; fill-column: 78;-*- Summary of significant changes to CCP4 at version 6.1.24 ("") --------------------------------------------------------------------------- * Program changes: * BUCCANEER: updated to 1.5 * POINTLESS: updated to 1.5.6 * Library changes: * MMDB: updated to 1.23 * CCTBX: updated to * Graphical User Interface: * Bugs fixed: * various build problems with shared libraries Summary of significant changes to CCP4 at version 6.1.13 ("Austwick") --------------------------------------------------------------------------- * Program changes: * BUCCANEER: updated to 1.4 * Library changes: * CLIPPER: update to 2.1 * Graphical User Interface: * BUCCANEER_REFMAC: updated include cycling 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 * REFMAC: updated to 5.5.0109 * MOLREP: updated to 10.2.35 * SFCHECK: updated to 7.3.16 * POINTLESS: updated to 1.4.2 * CTRUNCATE: updated to 1.0.11 * Library changes: * MMDB: update to 1.21 * 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 " option, which attempts to automatically copy any tasks previously installed in the CCP4 installation in , 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 or C multimer ( = 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