Building etc
Program changes
Library
Graphical User Interface

• Fixed problem with configure not detecting existing LAPACK and/or BLAS libraries from earlier CCP4i installation.

Program changes:

• CIF2MTZ: fixed broken LABOUT keyword.
• COMBAT: fixed bug with processing XDET, YDET and ROT values.
• IPDISP: fixed problem with failure of script under Tru64.
• MOLREP: fixed broken RAD keyword.
• PEAKMAX: fixed problem with misaligned atom name for OUTPUT PDB.
• PROFESSS: fixed broken TIDY keyword.
• SCALA: version 3.1.20
• SFTOOLS: fixed bug which failed to convert CNS Rfree to MTZ if the file contains reflections with zero sigma.
• SIGMAA: fixed problem with PARTIAL DAMP weights not being applied when keyword DAMP is in lower case.

Library:

• MTZLIB: fixed problem with uninitialized variable in s/r LRASSN (caused runtime errors associated with label assignments).

Graphical User Interface:

• Version 1.3.9.
• General: database.def is validated when changing projects.
• General: database.LOCK is only removed by the process that "owns" it.
• General: fixed problem with files missing from the "View Files from Job" list, for some long-running jobs (e.g. ARP/wARP).
• General: fixed anomalous behaviour when closing task windows (introduced accidentally in 1.3.8).
• Beast task: fixed problem with parameters being changed when trying to rerun earlier Beast jobs.
• DMMulti task: fixed problem with running multiple domain jobs.
• FFT task: fixed broken facility excluding sf's below a certain amplitude.
• Molrep task: fixed broken option to input fixed monomers.
• Monomer Library Sketcher: fixed problems with output for aromatic bonds, and with mixed cases for atom names.
• PrepHAData task: fixed broken option using "SAD data as Dano" and outputing SHELX format.
• SigmaA task: fixed broken options "combine isomorphous phase with partial solution" and "combine two sets of MIR phases".

INDEX

Building etc
Program changes
Library
Graphical User Interface

• 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:

• CCIFLIB: fixed bug with passing fixed length for Fortran strings in s/r ccp4ccif_setup_context.
• MAPLIB: five of the ENTRYs have been renamed 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 1.3.7.
• 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.

INDEX

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

• 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 7.1.
• 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.def) 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:

• toxd.mtz, rnase18.mtz and rnase25.mtz now distributed as well as .na4 files.