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. Skip step 1 if you have already installed CCP4 update No 4.

1. Replace the old version of $CCP4/bin/ccp4um-bin with the new one:

2. Download and un-compress the update directory:

Then, EITHER

3a. use the command line:

ccp4um -uri path-to-update-directory

OR

3b. use the graphic mode:

Launch ccp4um; 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: 6.5.001
Date: 24.12.14

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
acedrgadded ccp4i task interfaceyesyesyesyes
further improvementsyesyesyesyes
amplefixed executable pathyesyesyesyes
ccp4-basefixed setup script to unset unnecessary system variablesyesyesyesyes
ccp4iadded acedrgyesyesyesyes
ccp4-progsin pdbcur, added options to remove chain, TER record etcyesyesyesyes
crank2fixed interaction with pdbcuryesyesyesyes
documentationupdated for pdbcur and privateeryesyesyesyes
libccp4fixed ccp4 versioning, which, in particular, affected privateeryesyesyesyes
privateerminor changes for i2yesyesyesyes
xia2fixed -3d optionyesyesyes-

Update ID: 6.5.002
Date: 22.01.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
crank2several bug fixes, mainly related to the graphical interface and Crunch2yesyesyesyes
clipper-progsctruncate - fixes for issue with twinning alpha calculationyesyesyesyes
cmapcoeff - fix for issues with anomalous calculationyesyesyesyes
phaserphaser 2.5.7 - update to 2.5.7yesyesyesyes
blendFixed a bug in keywords management; now accepting both uppercase and lowercase. Fixed a bug for the calculation of aLCV.yesyesyesyes
privateerMinor bugfixesyesyesyesyes
monomersSeveral bug-fixes and addition of new compoundsyesyesyesyes
ccp4-progszanuda: adjustments to changes in refmac output pdb-file; bypass for P1 refinement failureyesyesyesyes
ccp4iMrSHELXE: temporarily switched off pdb- and mtz-files crosscheckyesyesyesyes
Fix for handling Protein/DNA complex sequences in Matthews interfaceyesyesyesyes
Fixed bug in refmac interface, which caused the rigid body folder to be empty, and other folders to display incorrect fieldsyesyesyesyes
documentationMinor fixesyesyesyesyes
mrbumpFix for sftools path length problem and Mac fix for MAFFTyesyesyesyes

Update ID: 6.5.003
Date: 13.02.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
refmac5resolve problem with occupancy refinementyesyesyesyes
imosflm7.1.2, bug fixesyesyesyesyes
mosflm7.1.2, bug fixesyesyesyesyes
pisa/qtpisafix bug in calculation of symmetry IDs for assembled monomersyesyesyesyes
Molrepimprove multi-copy searchyesyesyesyes
pointless1.9.25, bug fixesyesyesyesyes
aimless0.5.2, bug fixesyesyesyesyes
feckless0.0.5, bug fixesyesyesyesyes
ctruncate1.16.9, catch 0 sigmayesyesyesyes
ccp4irename mrshelxe to shelxe4mryesyesyesyes
sfcheckbug fixesyesyesyesyes
monomerscorrections and new monomersyesyesyesyes
ccp4-basefixed setup scripts for MANPATHyesyesyes-

Update ID: 6.5.004
Date: 23.02.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
pointless1,9.27, update polarization correction for XDS INTEGRATE with vertical spindleyesyesyesyes
aimless0.5.4, Fix bug in save/restore for factor offyesyesyesyes
bug fix for Scalepack file if one of I+ or I- are missingyesyesyesyes
refmacfix for bug in hydrogen generationyesyesyesyes
updateraddition of offline modeyesyesyesyes

Update ID: 6.5.005
Date: 10.03.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
ccp4srsupdated dictionaryyesyesyesyes
ccp4mg2.10.4, various bug fixesyesyesyesyes
ccp4ifix for shelxe4mr name change issuesyesyesyesyes
libg-related updates to the refmac guiyesyesyesyes

Update ID: 6.5.006
Date: 14.03.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
ccp4-progsareaimol - bug fixesyesyesyesyes
r500 - updateyesyesyesyes
standard_geometry.cif - updateyesyesyesyes
imosflmupdate to 7.1.3yesyesyesyes
mosflmupdate to 7.1.3yesyesyesyes
Molrepfix for bug in multi-copy searchyesyesyesyes
aimless0.5.7, bug fixesyesyesyesyes
privateerextended support for disaccharidesyesyesyesyes
adds support for external validation stringsyesyesyesyes
prosmartminor update to h-bond restaint generationyesyesyesyes
mmdb2update to rwbrook interfaceyesyesyesyes
ccp4iupdated autoSHARP interfaceyesyesyesyes

Update ID: 6.5.007
Date: 02.04.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
rwcontentssupport for strict NCS records, via pdb headeryesyesyesyes
blendupdate to 0.6.3yesyesyesyes
ccp4mgaddition of pdbviewyesyesyes-
pointlessBug fixesyesyesyesyes
update to 1.9.29yesyesyesyes
prelyscarBug fixes, documentation fixesyesyesyesyes
imosflmfix for issue with 0 oscillation angleyesyesyesyes
acedrgUpdateyesyesyesyes
atoms_electron.libElectron scattering terms for use in refmac (cyro-EM)yesyesyesyes

Update ID: 6.5.008
Date: 16.04.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
ARP/wARP1. Solvent search run from ccp4iyesyesyes-
2. The length of the file names in ligand searchyesyesyes-
3. Selection of MTZ column labels for protein model buildingyesyesyes-
Molrepimprove multi-copy search (nmr=4)yesyesyesyes
aimless0.5.8yesyesyesyes
bug fix for case SCALES CONSTANT BROTATION with one run (not sensible anyway)yesyesyesyes
fixed bug when there are different resolution limits for different datasetsyesyesyesyes
ccp4iupdated autosharp interfaceyesyesyesyes
updated blend interfaceyesyesyesyes
privateerbug fixesyesyesyesyes
clipperFix bug reading anomalous data from cif fileyesyesyesyes
imosflmfix for atan issueyesyesyesyes
dimplebug fixesyesyesyesyes
ccp4-progsupdate seqwtyesyesyesyes
lsqkab, improve handling of nucleic acids and increased dimensionsyesyesyesyes
documentationupdatesyesyesyesyes
acedrgfall back values of bonds addedyesyesyesyes
blendupdate to 0.6.6 01/04/2015yesyesyesyes
Added two columns in file "CLUSTERS.txt" which tell two datasets having current values of LCV and aLCV (module blend1.R).yesyesyesyes
Fixed bug for mode "-g D". Now data sets at the bottom are printed correctly (module blend4.R).yesyesyesyes

Update ID: 6.5.009
Date: 14.05.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
ARP/wARPactivation of postinstall script for use of standalone arp/warpyesyesyes-
crank2several bugfixesyesyesyesyes
jsrviewnew javascript outputyesyesyesyes

Update ID: 6.5.010
Date: 21.05.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
refmacvarious bug fixes and new program header2matryesyesyesyes
prosmartfixed issue with degenerate PDB filesyesyesyesyes
pointless1.9.31, allow real-space reindex operatorsyesyesyesyes
aimless0.5.9 make ABSORPTION lmax work. Bug fix in RESTORE with TILESyesyesyesyes
ctruncatefix for output column names issueyesyesyesyes
blend0.6.7, Fixed a bug responsible for the deletion of any file whose name includes referenceyesyesyesyes
libgdps for stacking planes of DNA/RNAyesyesyesyes
examplescorrections python.exam, pyrogen.exam and gere.seqyesyesyesyes
documentationupdate aimless and pointless documentationyesyesyesyes

Update ID: 6.5.011
Date: 10.06.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
ARP/wARP1. Fixed rare problem with handling space group p22121yesyesyes-
2. Improved input to Refmac for application of solvent maskyesyesyes-
mmdb2Corrected Link record in PDB header (incl. mmCIF i/o)yesyesyesyes
Blendupdate to 0.6.8yesyesyesyes
Fixed a "nasty" (and wrong piece of code!) bug in routine okRadDam that would make data sets with less than 6 images still undergo radiation damage routine (module blend1.R).yesyesyesyes
Ampleupdate to 1.0.0, gives windows supportyesyesyesyes
MrBUMPMainly improvements to support update to AMPLE and for new GUI2 interfaceyesyesyesyes
ccp4iupdated ample interfaceyesyesyesyes
theseusupdate to 3.3.0yesyesyesyes

Update ID: 6.5.012
Date: 29.06.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
jsrviewEnhanced outputyesyesyesyes
acedrgMajor updateyesyesyesyes
RDkit used for serveral tasksyesyesyesyes
protonation/deprotonation on serveral functional groups controlled by pH/pKayesyesyesyes
updates to internal bond/angle tablesyesyesyesyes
pisafix for pdb download issueyesyesyesyes
dimpleBug fixesyesyesyesyes
sfcheckfix for output mtzfile for non-standard settingsyesyesyesyes
refmac5fix for memory leak in SIRAS routinesyesyesyesyes
libgfix related to PDB files with insertion codesyesyesyesyes
imosflm/mosflmupdate to 7.2.0yesyesyesyes

Update ID: 6.5.013
Date: 03.07.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
ccp4-progsseqwt: sequence line length set to 1000yesyesyesyes
zanuda: updateyesyesyesyes
clipperCorrection to setting of NaN on some systemsyesyesyesyes
Fixes cbuccaneer crash on windows---yes
monomersvarious correctionsyesyesyesyes
pointlessupdate to 1.9.33yesyesyesyes
aimlessupdate to 0.5.12yesyesyesyes
ccpiupdate to aimless taskyesyesyesyes
imosflmfix for issue with parallel processing in 7.2.0yesyesyesyes
documentationvarious updatesyesyesyesyes

Update ID: 6.5.014
Date: 03.08.15

Component Description Mac OS X 64-bitLinux 32-bitLinux 64-bitWindows
molrepcorrection to CC in TF calculationyesyesyesyes
blend0.6.10, aLCV has priority over LCVyesyesyesyes
pointless1.10.5, imporved resolution estimate for point-group estimationyesyesyesyes
acedrgmake sure formal changes are consistent with input files when atoms are not in functional groupsyesyesyesyes
correct name convention for H atomsyesyesyesyes
gesamt1.02, includes multiple alignmentyesyesyesyes
Bug fixesyesyesyesyes
ccp4-progsfreerflag, update random seed to ensure uniform distributionyesyesyesyes
documentationupdate gesamt and freerflagyesyesyesyes

Reporting bugs

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