CCP4 v4.1 Program Changes

INDEX

Building etc
Program changes
Library
New programs
Graphical User Interface
Documentation
Withdrawal

• 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.

• 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.