CCP4 v6.2.992 Program Changes

POINTLESS: updated to 1.3.9
SCALA: updated to 3.3.15
REFMAC5: updated to 5.5.0101. 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

CCP4 v6.1.1 Program Changes

INDEX

intel 11: mostly supported

Program changes:

PDB_EXTRACT: updated to 3.004
REFMAC5: updated to 5.5.0071
POINTLESS: updated to 1.3.1

Library changes:

MMDB: update to 1.19
monomer dictionaries: various updates, including CYS-MPR

Updated interfaces:

REFMAC55: better integration of SAD refinement
BP3: interface added

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
3648: REFMAC5 interface: failure to adjust NCS weights
3596: IMOSFLM: requires project directory to exist, fails otherwise
3630: SCALEPACK2MTZ: does not read symmetry from input file

CCP4 v6.1.0 Program Changes

INDEX

Graphical User Interface

Documentation

Withdrawal

Examples

A list of general acknowledgements for testing CCP4 v6.1.0 can be found here.

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)