CCP4 Updates

1. Cumulative update patches

These patches need not to be used if automatic updates work fine for you. If, for any reasons, automatic updates do not work for you or you prefer updating your CCP4 setup manually, download the following arhives and unpack them into the CCP4 directory:

Mac OS X 64-bit:   ccp4-6.4.0-patch-macosx_x86_64.tgz
Linux 32-bit:   ccp4-6.4.0-patch-linux_x86.tgz
Linux 64-bit:   ccp4-6.4.0-patch-linux_x86_64.tgz
Windows:   ccp4-6.4.0-patch-windows_x86.zip

2. Updates Summary

Update ID: 6.4.0-001
Date: 25.10.13

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
CCP4fixes to Qt libraries critical for some Mac OSX setupsyes---
fixes to Qt libraries critical for using on KDE desktops-yesyes-
TclTknow works on CentOS4-yesyes-
added missing libraries to make fresh ccp4 installation work without rebooting---yes
Cootfixed keyboard shortcutsyes---
now runs without sourcing ccp4-yesyes-
MrBUMPfixed MAFFT optionyesyesyesyes
AMPLEadded subtask for membrane proteins; bug fixes for Macyesyesyes-
Xia2update to release 0.3.6.3 (fixes ctruncate issue)yesyesyes-
QtRViewfixes allowing display of large summaries, e.g. aimlessyesyesyesyes
iMosflmfixes critical issue on 32 bit linuxes-yes--

Update ID: 6.4.0-002
Date: 20.11.13

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
CCP4 UpdateA technical update allowing uninstallation of the broken update No 2yesyesyesyes

Update ID: 6.4.0-003
Date: 20.11.13

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
CCP4 UpdateBug fixesyesyesyesyes
Increased maximum waiting time for background update check in CCP4Iyesyesyesyes

Update ID: 6.4.0-004
Date: 20.11.13

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
ARP/wARP1. The use of non-crystallographic symmetry for protein chain tracing has been enabled (it was accidentally disabled in version 7.4)yesyesyes-
2. The "SAD refinement protocol" (Murshudov et al 2011) has undergone many fixes and now works wellyesyesyes-
3. The routine for ligand identification has been made faster and some small bugs been fixedyesyesyes-
4. A few bugs have been fixed in the ARP/wARP installer and shell-specific problems sometimes occurring on Linux should now be curedyesyesyes-
5. The manual has been updatedyesyesyes-
MolrepNew interfaceyesyesyesyes
MrBUMPA new option of model re-building after SHELXEyesyesyesyes
A fix for phaser_sculptor dispatcheryesyesyesyes
Fixed Sun Grid Engine cluster job submission problemsyesyesyesyes
Xia2Update to release 0.3.6.3 (fixes ctruncate issue)---yes
pointlessBug fixesyesyesyesyes
aimlessBug fixesyesyesyesyes
ctruncateBug fixesyesyesyesyes
ViewHKLAdditional visual control to enhance weak reflectionsyesyesyesyes
Bug fixesyesyesyesyes
QtRviewNow finds Coot executable automaticallyyes---
Bug fixesyesyesyesyes
ccp4iFixed path to mmcif library enabling e.g. harvesting option of old truncateyes---
Fixed task interfaces for bp3 and crunch2yesyesyesyes
Now can be installed and used on a network drive---yes

Update ID: 6.4.0-005
Date: 02.12.13

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
DocumentationAdded documentation for Othercell and updated documentation for Pointless and Aimlessyesyesyesyes
cprodrgFix for segfault on OSXyes---
ctruncateBetter handling of resolution limits for testsyesyesyesyes
AimlessInclusion of history in mtzyesyesyesyes
PointlessFix axial reflection bugyesyesyesyes
CrankFixes for use of ARP/wARP 7.4yesyesyesyes

Update ID: 6.4.0-006
Date: 21.12.13

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
freerflagAdded option of assigning identical Free-R flag to twin-related reflectionsyesyesyesyes
QtRViewFixed report page for Phaser---yes
MrBUMPFix for SCOP search results error when chain is removed for zero lengthyesyesyesyes
Added option to disable ctruncate stepyesyesyesyes
Fixed a minor bug in the ctruncate stepyesyesyesyes
ViewHKLBring unmerged code in line with current Pointless and Aimlessyesyesyesyes
Print phases in degrees not radiansyesyesyesyes
Return filetype for non-MTZ files (for ccp4i2)yesyesyesyes
Cope with inverted column order in mtz-fileyesyesyesyes
ctruncateFixed missing program name in outputyesyesyesyes
ccp4-coreAdded missing legacy program xplot84driveryesyesyes-
ExamplesCorrected data files toxd_old.mtz and aucn.scayesyesyesyes
Technical changes to run-all script and regression testsyesyesyesyes
ccp4-progsMinor fixes in domain2chain and vectors for strict compilersyesyesyesyes
Minor fixes in sapi for strict compilersyesyesyes-
Technical changes to ccp4-python, imosflm and zanuda scriptsyesyesyesyes
GUI-2Technical update adding cmtzjoin and cmtzsplit programs for ccp4i2yesyesyesyes

Update ID: 6.4.0-007
Date: 17.01.14

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
pointlessfixed crash when using reference data with no alternative indexingyesyesyesyes
with multiple files, include columns present in any fileyesyesyesyes
added crash message for running out of memoryyesyesyesyes
fixed bug in XML graphs for ccp4i2yesyesyesyes
fixed (rare) crash if there are only 2 axial reflectionsyesyesyesyes
aimlessfixed NBINS option for multiple datasetyesyesyesyes
added crash message for running out of memoryyesyesyesyes
fixed bug in XML graphs for ccp4i2yesyesyesyes
ctruncatedefensive codes added to estimation of twin fraction from L-test and Murray-Rust plotyesyesyesyes
corrected typosyesyesyesyes
molreprelaxed restrictions due to cell dimensions on integration radius in SRFyesyesyesyes
corrected beta range for LRF from 90 to 180yesyesyesyes
all occupancies in xyzout are now set to 1yesyesyesyes
extinct harmonic coefficients set to zero in RFyesyesyesyes
ccp4imolrep: corrected nmon and added np2, nml and score widgetsyesyesyesyes
crunch2 and bp3: corrections for new file layoutyesyesyesyes

Update ID: 6.4.0-008
Date: 14.02.14

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
PhaserNow uses new MMDByesyesyesyes
Many bug fixes, version 2.5.6yesyesyesyes
Phaser_EP interface correction for hyssyesyesyesyes

Update ID: 6.4.0-009
Date: 28.02.14

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
areaimolFix to atom records of output pdb.yesyesyesyes
mrbumpSeveral fixes including bug fixes to allow SHELXE to run when submitting jobs to a cluster.yesyesyesyes
theseusTheseus now distributed with CCP4 for use in AMPLE.yesyesyesyes
spickerSpicker now distributed with CCP4 for use in AMPLE.yesyesyesyes
fecklessA new auxiliary program for the forthcoming multi-lattice version of imosflm.yesyesyesyes
ampleFix for NMR re-modelling option and Scwrl can be run as an additional step.yesyesyesyes
freerflagFixed non-equal subsets for different free-R-flag values when the COMPLETE keyword is used. Updated the documentation.yesyesyesyes

Update ID: 6.4.0-010
Date: 07.03.14

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
ARP/wARP1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent buildingyesyesyes-
2. Fix in the identification of non-crystallographic symmetry that in some cases led to zero target number of residuesyesyesyes-
3. Fix in recognition of secondary structural elements that in rare cases led to a 'bus error'yesyesyes-
* Many thanks to Marcin Cymborowski, Carmelo Giacovazzo, Ulrich Gohlke and Vito Calderone for reporting these problem cases.yesyesyes-
imosflmupdate to 7.1.0yesyesyesyes
Multi-lattice implementationyesyesyesyes
Parallel processing of wedgesyesyesyesyes
fecklessupdate to 0.0.2yesyesyesyes
Fixes several major bugsyesyesyesyes
pointlessupdate to 1.9.1yesyesyesyes
General update for multi-latticeyesyesyesyes
ctruncateupdate to 1.13.13yesyesyesyes
Fixes negative eigenvalue exit during anisotropy analysisyesyesyesyes
cnautilusupdate to version 0.4yesyesyesyes
Some basic output markup and numbering of output sequencesyesyesyesyes
refmac5update to version 5.8.006yesyesyesyes
Fixes for ARP/wARP and forthcoming release of Crank2yesyesyesyes

Update ID: 6.4.0-011
Date: 10.03.14

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
imosflmfixed check of ipmosflm versionyesyesyes-
bug fix in launch script for csh and tcshyesyesyes-
now includes correct ipmosflm version 7.1.0---yes

Update ID: 6.4.0-012
Date: 28.03.14

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
crank2New SAD phasing pipelineyesyesyesyes
monomer libraryCorrections to OXY, PO4 and UREyesyesyesyes
imosflmUpdate to version 7.1.1yesyesyesyes

Reporting bugs

All bugs should be reported to ccp4@stfc.ac.uk.