CCP4 v5.0 Program Changes

INDEX

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

A list of general acknowledgements for testing CCP4 v5.0 can be found here.

• 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_ecc [options]"
• gnu compilers: IA64 support implemented; use "configure linux [options]" (warning 3.0 broken)
• gnu compilers: FreeBSD build can use g77 (thanks 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.
  
• MOLREP: Molrep now uses keywords and command line options. Also updated to verion 8.2.01.
• MOSFLM: new version 6.2.4
• OASIS: new version 1.2.2.
• 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.
• 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 3.2.4
• 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:

• 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.
• Import Scaled Data: added option to keep intensities in output MTZ file.
• 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

• 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".