CCP4 Updates

Update packages

The tarballs linked to this page are for use with CCP4 updater (ccp4um) in off-line mode (e.g. without network connection). You do not need them if your CCP4 update works normally through the internet.

Follow instructions below if you do intend to use the CCP4 updater in off-line mode.

1. Download and un-compress the update directory:

Then, EITHER

2a. use the command line:

ccp4um -uri path-to-update-directory

OR

2b. use the graphic mode:

Launch ccp4um available from CCP4 7.0 installation; answer "No" in the first dialog suggesting revision of proxy settings; press "OK" in the second dialog suggesting installation of updates from local update directory; navigate to the update directory in the file browser, select it and press "Choose". From this point on, ccp4um will operate as usual.

Updates summary

Update ID: 7.0.001
Date: 25.01.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
acedrgupdated tables and executableyesyesyes--
balbes-pipelineadded-yesyes--
ccp4ichanges associated with changes in ccp4um and crank2yesyesyes--
ccp4i2fixes for importing projectsyesyesyes--
refmac task: bond order added to ligands reportyesyesyes--
fix stopping unnecessary reading of MTZ fileyesyesyes--
fix type P2 21 21yesyesyes--
temporary fix to aimless_pipe FreeR testyesyesyes--
fix stopping possible crash on exit;yesyesyes--
fix for coping with data in external filesyesyesyes--
added 'Quick Expert' and Youtube links to Help menuyesyesyes--
Please pick up update 4588 from ccp4i2 trunk.yesyesyes--
buccaneer pipeline: BFAC restraints reverted to refmac defaultsyesyesyes--
fixed sporadic failures to reopen New project windowyesyesyes--
changes associated with changes in ccp4umyesyesyes--
ccp4mgfix for using Gesamt in superpose taskyesyesyes--
crank2added scaleit; other fixesyesyesyes--
dialsfixed dials.reciprocal_lattice_vieweryesyesyes--
monomersadded 1774 entries generated with acedrgyesyesyes--
curated several entriesyesyesyes--
mrbumpupdated database for PDB sequencesyesyesyes--
qt4Added missing QtDBus library required for some platforms-yesyes--

Update ID: 7.0.002
Date: 02.02.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
MolrepBug: fixed integration radius dependence on unit cellyesyesyes--
prosmartBug: bug fixesyesyesyes--
ampleBug: Bug fixesyesyesyes--
acedrgBug: Bug fixesyesyesyes--
clipperBug: remove unnecessary file readsyesyesyes--
updaterBug: Bug fixesyesyesyes--
ccp4i2Bug: validate geometry - fix for issue with multiple conformationsyesyesyes--
Bug: ccp4mg launch - fix for issue on windowsyesyesyes--
Bug: crank2 output fixesyesyesyes--

Update ID: 7.0.003
Date: 11.02.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
ccp4i2fixed update dialog window launching every time a new project window opensyesyesyes--
setupfixed update manager for windows 64-bit accessing incorrect directory on serveryesyesyesyesyes

Update ID: 7.0.004
Date: 26.02.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
documentationupdate: update to privateer documentationyesyesyesyesyes
ccp4i2privateer interface - fixed a bug with three letter codes not being passed to Privateeryesyesyesyesyes
bug - fix for overly aggressive update messagesyesyesyes--
viewhklupdate 0.0.2 - reflectionlist updates and set intensity for unmerged filesyesyesyesyesyes
ccp4iupdate: phaser interfaces updateyesyesyesyesyes
phaserbug fixesyesyesyesyesyes
cootfix mixed libpng statusyes----
aimlessnew version 0.5.23yesyesyesyesyes
ccp4mgfixes problems with NMR models in MrBUMP interfaceyesyesyesyesyes
fixes batch rendering when CCP4 is on different drive from output file---yesyes
pointlessXML fixesyesyesyesyesyes
monomersadded and corrected several monomersyesyesyesyesyes
removed duplicated monomer COM to fix JLigandyesyesyesyesyes
mrbumpupdated for running in CCP4i2 on Windowsyesyesyesyesyes

Update ID: 7.0.005
Date: 08.03.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
ccp4ifixed communication with WinCoot---yesyes

Update ID: 7.0.006
Date: 18.03.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
ctruncateupdate to 1.17.9yesyesyesyesyes
blendupdate to 0.6.19yesyesyesyesyes
clipper-pythonconflict between matrixRow class from ccp4mg and clipper-pythonyesyesyesyesyes
documentationfreerflag documentation updateyesyesyesyesyes
pisaupdateyesyesyesyesyes
xia2include missing xia2_pychef_ext.soyesyesyesyesyes
xia2 bug fixyesyesyesyesyes
crank2bug fixesyesyesyesyesyes
ccp4i2display database icon on dictionary selection widget in Coot taskyesyesyesyesyes
Fix locale issues in linux startup scriptsyesyesyesyesyes
Better display of the Input tab for seelcted sub-jobsyesyesyesyesyes
Remove View/Edit from Dictionary file menuyesyesyesyesyes
Fix 'View in CCP4mg' for Refmac tasksyesyesyesyesyes
ccp4i2 imosflm interface: pass job directory to imosflm so output goes in correct locationyesyesyesyesyes
Fixes failure to run on some SUSE linux and forces "C" locale to avoid internationalization problemsyesyesyesyesyes
mmdb2MMDB updateyesyesyesyesyes
viewhklupdateyesyesyesyesyes
qtlibsupdateyesyesyesyesyes
choochpreviously missing---yesyes

Update ID: 7.0.007
Date: 24.03.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
dialsupdate to release 1.1yesyesyesyesyes
cctbxupdate to 17 March 2016 versionyesyesyes--

Update ID: 7.0.008
Date: 05.04.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
monomersChirality fix in 5UJ, PMR; format fix B1Z; added 47K, 5TW, 5UOyesyesyesyesyes
clipper-python}Fixes matrix element accessyesyesyes--
Xia2Update to release 0.3.6.3 (fixes ctruncate issue)---yesyes
pointlessupdate to 1.10.21yesyesyesyesyes
trap non-overlap between data and referenceyesyesyesyesyes
improved resolution limit robustnessyesyesyesyesyes
aimlessupdate to 0.5.24yesyesyesyesyes
fix bug if different resolutions for different runs. Small bug fix in secondary beam scaling. Switch off secondary scaling in first pass, stabilises the scaling in some cases. Trap negative scales (shouldn't happen). Fixes to sample SDs (for high multiplicity), compare sample SD to propagated SD. Output secondary beam corrections to logfile and XML. Reset SdFac after first round scalingyesyesyesyesyes
pisaGeneration of complete remarks 300 and 350yesyesyesyesyes
ccp4i2Make modern style the defaultyesyesyesyesyes
Fix for FreeR flag generation when one already existsyesyesyesyesyes
Fix import merged performing aimless analysis on intensities when user has selected Fsyesyesyesyesyes
ccp4ilocate clustalw2 for alignment taskyesyesyesyesyes

Update ID: 7.0.009
Date: 06.04.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
cootupdate to version 0.8.3yesyesyes--

Update ID: 7.0.010
Date: 11.04.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
blendupdate to 0.6.20yesyesyesyesyes
Fixed annoying halting of the program in endless loop when asking for dendrogram-type graphics (graphics mode). Now the deepest possible level is always selected even when the user chooses an higher level. Output in "graphics" directory has also level index limited to deepest level, no matter what user decides.yesyesyesyesyes
Increased formatting space for I and sigI in "refs_*_*.dat" files.yesyesyesyesyes
acedrgupdated internal tables for bonds and anglesyesyesyesyesyes
the version working under Windows systemyesyesyesyesyes
Xia2(experimental) turn off multiprocessing---yesyes
aimless0.5.25 undoes nasty introduced in 0.5.24yesyesyesyesyes
documentationupdate pointless, aimless and dimple documentationyesyesyesyesyes
cootcorrect for renaming of findwaters and findligand binaries, and relocation of mini-rsryesyesyes--

Update ID: 7.0.011
Date: 27.04.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
ccp4i2major updateyesyesyesyesyes
dialsupdate to 1.1.3yesyesyesyesyes
libccp4add P 1 21/n 1 to symop.libyesyesyesyesyes
arcimboldoextended options in ccp4i interfaceyesyesyes--
connection to remote gridyesyesyes--
molrepminor update aimed at EMyesyesyesyesyes
sfcheckfix for reading of EM mapsyesyesyesyesyes

Update ID: 7.0.012
Date: 06.05.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
refmacFc(anom) is now calculated if ANOM MAPO is usedyesyesyesyesyes
pointlessupdate to 1.10.25yesyesyesyesyes
More robust alternative indexing checks to previous fileyesyesyesyesyes
Allow combination of multiple merged files into an unmerged fileyesyesyesyesyes
Added extra optional headers to free-format input filesyesyesyesyesyes
jsrviewimproved efficiency for jobs with many calls to rvapiyesyesyesyesyes
ctruncate1.17.14: update anomalous warningsyesyesyesyesyes
libgbug fixesyesyesyesyesyes
ccp4i2updated import_mergedyesyesyesyesyes
libccp4something for Harryyesyesyesyesyes

Update ID: 7.0.013
Date: 17.05.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
dialsDIALS 1.2.0yesyesyesyesyes
Support for EIGER datayesyesyesyesyes
Outlier rejection for centroid refinement now in blocksyesyesyesyesyes
dials.discover_better_experimental_model now uses random subset of reflections from entire scanyesyesyesyesyes
xia2xia2 0.4.0.335yesyesyesyesyes
Support for EIGER data in -dials and -3d pipelines (latter requires H5ToXDS)yesyesyesyesyes
xia2.html report automatically generated after successful completion of xia2yesyesyesyesyes
DIALS pipeline now includes DIALS beam centre searchyesyesyesyesyes
xia2.to_shelx can use output of xia2.get_unit_cell_errors and generate cif fileyesyesyesyesyes

Update ID: 7.0.014
Date: 24.05.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
ARP/wARPUpdate for operation with new refmacyesyesyes--
refmacscaling and many other bugs were removed to to make sure that arp/warp works without problemyesyesyesyesyes
Multiple sharpeinging/blurring options have been added. These are for EM maps as well as crystallographic mapsyesyesyesyesyes
Many features have been addedyesyesyesyesyes
ccp4i2fixes for coot interfaceyesyesyesyesyes
aimless0.5.26, speed up of SF calculationyesyesyesyesyes
cootreading of anomalous mapsyesyesyesyesyes
monomersChirality fix in RG1; multiple fixes for ASX, GLX; format fix in 0KA; replaced 51P; added 46W, 4B7, K3G, VVA, XP5yesyesyesyesyes
gesamt1.13: detail CSV reports, inclusion/exclusion lists and trim options for pdb scansyesyesyesyesyes
documentationupdate for aimless and pointlessyesyesyesyesyes
ccifupdate of mmcif dictionary to 4.064 (3/5/16)yesyesyesyesyes

Update ID: 7.0.015
Date: 17.06.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
ccp4mgUpdated MrBUMP interfaceyesyesyesyesyes
N-/O-glycosylation selection menusyesyesyesyesyes
New glycan vieweryesyesyesyesyes
privateerN- and O- glycan structure validationyesyesyesyesyes
reworked stereochemistry detectionyesyesyesyesyes
generates SVG diagrams of glycansyesyesyesyesyes
many bug fixesyesyesyesyesyes
ccp4i2new privateer interfaceyesyesyesyesyes
mrbumpupdates to include better scoring and ensemblingyesyesyesyesyes
ampleNew modularised version of AMPLEyesyesyesyesyes
pointless1.10.27: accurate averaging of wavelengthyesyesyesyesyes
aimless0.5.27: accurate averaging of wavelengthyesyesyesyesyes
ccp4iupdate ample interfaceyesyesyesyesyes
gesamtupdate to domain identificationyesyesyesyesyes

Update ID: 7.0.016
Date: 24.06.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
refmac5bug fixesyesyesyesyesyes
monomersmore monomers and correctionsyesyesyesyesyes
ccp4i2update buccaneer pipeline and add shelxeMRyesyesyesyesyes
buccaneerupdate to 1.6.3yesyesyesyesyes
molrepaniso correction improvementyesyesyesyesyes
sfcheckaniso correction improvementyesyesyesyesyes
blendupdate to 0.6.21yesyesyesyesyes
ViewHKLdeal with names including slashesyesyesyesyesyes
dimpleadjust parsing of pointless output for changes in pointless 1.10.22yesyesyesyesyes
documentationupdate blend documentationyesyesyesyesyes
ARP/wARPUpdate for operation with new refmacyesyesyes--

Update ID: 7.0.017
Date: 07.07.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
arcimboldofix for space group C121yesyesyes--
ccp4-progsfreerflag: fix forunit cell parameters inconsistent with the space groupyesyesyesyesyes
lorestradded Windows support---yesyes
introduced parallelisation and corresponding changes made in ccp4iyesyesyesyesyes
jsrviewfixed widget removalyesyesyesyesyes
fixed dynamic display of several files in separate tabsyesyesyesyesyes
option of putting report page as divyesyesyesyesyes
dialsfixed export_bitmapsyesyesyesyesyes

Update ID: 7.0.018
Date: 12.08.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
ccp4i2improved menu and task responsivenessyesyesyesyesyes
fixes to SIRAS pipelineyesyesyesyesyes
remote job submissionyesyesyesyesyes
shelxe1. MRSAD (when shelxe reads name.pda and name_fa.hkl) was not working correctly. This was reported by Thomas Schneider.yesyesyesyesyes
2. There was an error in calculating the phase errors relative to a reference structure that was specific to the not very common space group F23, reported by Jens Thomas.yesyesyesyesyes
cootcoot 0.8.5yesyesyes--

Update ID: 7.0.019
Date: 06.09.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
dialsupdate to 1.3yesyesyesyesyes
xia2update to 0.5yesyesyesyesyes
ccp4i2update for xia2 changesyesyesyesyesyes
cootlibpng issue correctionyes----

Update ID: 7.0.020
Date: 22.09.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
pisaupdate to version 2.0.9yesyesyesyesyes
crystal data is now written in output structure filesyesyesyesyesyes
ccp4i2optional use of native file browser and separate Download buttonyesyesyesyesyes
arcimboldofixed check for shelx versionyesyesyes--
pointlessupdate to 0.5.28yesyesyesyesyes
prosmartupdate to 0.853yesyesyesyesyes
Added additional support for nucleic acidsyesyesyesyesyes
cootupdate to 0.8.6yesyesyes--
correction to pyrogen python callyesyesyes--
ARP/wARPinstallation script is rerun in conjunction with CCP4 update 16yesyesyes--

Update ID: 7.0.021
Date: 14.10.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
panddaNew application: a multi-dataset electron density analysis approach to changed-state (e.g. bound ligand) identificationyesyesyes--
aimless0.5.28 format change to RunPairs to avoid coalescence of columnsyesyesyesyesyes
ccp4i2Improvements to remote running and enable customised remote runningyesyesyesyesyes
Add 'Show jobs and processes' option to the Utilities menuyesyesyesyesyes
Add option to copy job parameters into a task.yesyesyesyesyes
More automatic cleanup of temporary files on closing down CCP4i2yesyesyesyesyes
Fix 'Project manager' issue that allowed a project to be its own parent (and disappear)yesyesyesyesyes
ccp4isuperpose-gesamt: corrected previously mixed fixed and moving moleculesyesyesyesyesyes
clipper-pythonfixes for ccp4i2yesyesyesyesyes
documentationdocumentation for panddayesyesyes-yes
update of blend documentationyesyesyesyesyes
pythonInclusion of standalone python for i2 to fix issues with links and crashes---yes-

Update ID: 7.0.022
Date: 18.11.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
shelxlupdateyesyesyesyesyes
phaserupdate to 2.7.17yesyesyesyesyes
xia2update to 0.5.57yesyesyesyesyes
dialsupdate to 1.3.5yesyesyesyesyes
cctbxupdateyesyesyesyesyes
arcimboldoUpdate for new phaseryesyesyesyesyes
updated ccp4i task interface for lite and added interfaces for borges and schredderyesyesyesyesyes
fixes for borges libraryyesyesyesyesyes
ccp4iUpdated phaser interfacesyesyesyesyesyes
bug fix: update manager on windows 10yesyesyesyesyes
ccp4i2update for new phaseryesyesyesyesyes
bug fix: added opt out for updatesyesyesyesyesyes
aimlessupdate to 0.5.29yesyesyesyesyes
pointlessupdate to 1.10.27yesyesyesyesyes

Update ID: 7.0.023
Date: 23.11.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
cootupdate to coot 0.8.7yesyesyes--
phaserBug fixes: ccp4i and interaction with Arcimboldoyesyesyesyesyes
Update: Improved treatment of systematically weak data (e.g. severe anisotropy)yesyesyesyesyes
ccp4ibug fix: phaser, updated defaults for phaser tasksyesyesyesyesyes
bug fix: mrbump, updated defaults for phaseryesyesyesyesyes
numpynumpy update for ccp4i2 python---yes-

Update ID: 7.0.024
Date: 26.11.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
cootfix: fix to coot auto-mutateyesyesyes--
pointless1.10.28 trap Nan in centrosymmetric probability (small molecule non-chiral)yesyesyesyesyes
crank2update: 2.0.132yesyesyesyesyes
refmacRefmac would confuse atoms names when a link between the same monomer names was defined.yesyesyesyesyes
monomersvarious updatesyesyesyesyesyes
blendupdate: blend version 0.6.22yesyesyesyesyes
ccp4i2update:updated crank2 pipeline 2.0.132yesyesyesyesyes
update:gesamt single chain alignmentyesyesyesyesyes
ccp4iupdate: updated crank2 interface 2.0.132yesyesyesyesyes

Update ID: 7.0.025
Date: 07.12.16

Component Description Mac OS 64-bitLinux 32-bitLinux 64-bitWindows 32-bitWindows 64-bit
MrBUMPGesamt-aligned ensembling addedyesyesyesyesyes
Bug fixesyesyesyesyesyes
dialsFixed configuration to repair xia2 and dials.image_vieweryesyesyes--
sfcheckFixed postscript outputyesyesyesyesyes
CCP4mgUpdate for MrBUMP model preparation supportyesyesyesyesyes
ccp4iUpdates to MrBUMP interfaceyesyesyesyesyes

Reporting bugs

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