CCP4 6.3.0 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:   ccp4-6.3.0-patch-macosx.tar.gz
Linux 32-bit:   ccp4-6.3.0-patch-linux-x86.tar.gz
Linux 64-bit:   ccp4-6.3.0-patch-linux_x86_64.tar.gz
Windows:   ccp4-6.3.0-patch-windows.zip

Built on 04.04.13

2. Updates Summary

Update ID Date Mac OS XLinux 32-bitLinux 64-bitWindows
6.3.0-02104.04.13 QtRView: Corrected Prosmart report page; enabled incorporation of web-links into citation section
QtRView: Corrected Prosmart report page; enabled incorporation of web-links into citation section
QtRView: Corrected Prosmart report page; enabled incorporation of web-links into citation section
QtRView: Corrected Prosmart report page; enabled incorporation of web-links into citation section
6.3.0-02026.03.13 Update Manager (ccp4um), QtRView: Technical update in preparation for the next release
Gesamt, Superpose: Corrections to the previous update (Now print superposition matrices also in fractional coordinates); better presentation in QtRView result viewer
Refmac, ProSmart: Results of superposition analysis and external restraints are now accessible through QtRView report
Update Manager (ccp4um), QtRView: Technical update in preparation for the next release
Gesamt, Superpose: Corrections to the previous update (Now print superposition matrices also in fractional coordinates); better presentation in QtRView result viewer
Refmac, ProSmart: Results of superposition analysis and external restraints are now accessible through QtRView report
Update Manager (ccp4um), QtRView: Technical update in preparation for the next release
Gesamt, Superpose: Corrections to the previous update (Now print superposition matrices also in fractional coordinates); better presentation in QtRView result viewer
Refmac, ProSmart: Results of superposition analysis and external restraints are now accessible through QtRView report
Update Manager (ccp4um), QtRView: Technical update in preparation for the next release
Gesamt, Superpose: Corrections to the previous update (Now print superposition matrices also in fractional coordinates); better presentation in QtRView result viewer
Refmac, ProSmart: Results of superposition analysis and external restraints are now accessible through QtRView report
6.3.0-01915.03.13 Aimless: Task interface fixed in part of input customisation section
Molrep: Improvements to scoring system and bug fixes
Logview: Command-prompt routine for viewing individual log files with QtRView. Simply call it with path to the log file as the only parameter
QtRView: Cosmetic improvements and changes for Logview
Gesamt: Now prints superposition matrices also in fractional coordinates
Superpose: Now prints superposition matrices also in fractional coordinates
Aimless: Task interface fixed in part of input customisation section
Molrep: Improvements to scoring system and bug fixes
Logview: Command-prompt routine for viewing individual log files with QtRView. Simply call it with path to the log file as the only parameter
QtRView: Cosmetic improvements and changes for Logview
Gesamt: Now prints superposition matrices also in fractional coordinates
Superpose: Now prints superposition matrices also in fractional coordinates
Aimless: Task interface fixed in part of input customisation section
Molrep: Improvements to scoring system and bug fixes
Logview: Command-prompt routine for viewing individual log files with QtRView. Simply call it with path to the log file as the only parameter
QtRView: Cosmetic improvements and changes for Logview
Gesamt: Now prints superposition matrices also in fractional coordinates
Superpose: Now prints superposition matrices also in fractional coordinates
Aimless: Task interface fixed in part of input customisation section
Molrep: Improvements to scoring system and bug fixes
Logview: Command-prompt routine for viewing individual log files with QtRView. Simply call it with path to the log file as the only parameter
QtRView: Cosmetic improvements and changes for Logview
Gesamt: Now prints superposition matrices also in fractional coordinates
Superpose: Now prints superposition matrices also in fractional coordinates
6.3.0-01805.03.13 Aimless Bug fixing in task interface
ccp4i Fixed long-standing issue on Linux and Mac: system Python was used instead of the one distributed with CCP4
QtPISA Added output of monomer, interface and assembly details in plain text; eliminated Qt widget flashing
Aimless Bug fixing in task interface
ccp4i Fixed long-standing issue on Linux and Mac: system Python was used instead of the one distributed with CCP4
QtPISA Added output of monomer, interface and assembly details in plain text; eliminated Qt widget flashing
Aimless Bug fixing in task interface
ccp4i Fixed long-standing issue on Linux and Mac: system Python was used instead of the one distributed with CCP4
QtPISA Added output of monomer, interface and assembly details in plain text; eliminated Qt widget flashing
Aimless Bug fixing in task interface
ccp4i Fixed long-standing issue on Linux and Mac: system Python was used instead of the one distributed with CCP4
QtPISA Added output of monomer, interface and assembly details in plain text; eliminated Qt widget flashing
6.3.0-01721.02.13 geomcalc io bug fixing in residue numbering
aimles fixes in Define Run section of the aimles task interface
Ample/MrBUMP now runs shelxd_mp in mp mode
geomcalc io bug fixing in residue numbering
aimles fixes in Define Run section of the aimles task interface
Ample/MrBUMP now runs shelxd_mp in mp mode
geomcalc io bug fixing in residue numbering
aimles fixes in Define Run section of the aimles task interface
Ample/MrBUMP now runs shelxd_mp in mp mode
geomcalc io bug fixing in residue numbering
pisa fixes for handling back slashes on windows
aimles fixes in Define Run section of the aimles task interface
Ample/MrBUMP now runs shelxd_mp in mp mode
6.3.0-01628.01.13 pdb_merge execution permission added
pdbcure execution permission added
pisa execution permission added, documentation corrected
aimless documentation corrected and added to index
mrBump documentation for QtRView added, SHELXE module adjusted to use intensities rather than amplitudes
pdb_merge execution permission added
pdbcure execution permission added
pisa execution permission added, documentation corrected
aimless documentation corrected and added to index
mrBump documentation for QtRView added, SHELXE module adjusted to use intensities rather than amplitudes
pdb_merge execution permission added
pdbcure execution permission added
pisa execution permission added, documentation corrected
aimless documentation corrected and added to index
mrBump documentation for QtRView added, SHELXE module adjusted to use intensities rather than amplitudes
pisa documentation corrected
aimless documentation corrected and added to index
mrBump documentation for QtRView added, SHELXE module adjusted to use intensities rather than amplitudes
QtRView fixed configuration bug, which caused Coot launching in wrong environment
6.3.0-01525.01.13 Aimless
Pointless
Ctruncate
Documentation updated following previous changes
Ctruncate Memory leak fixed
Aimless
Pointless
Ctruncate
Documentation updated following previous changes
Ctruncate Memory leak fixed
Aimless
Pointless
Ctruncate
Documentation updated following previous changes
Ctruncate Memory leak fixed
Aimless
Pointless
Ctruncate
Documentation updated following previous changes
Ctruncate Memory leak fixed
6.3.0-01418.01.13 Aimless Various bug fixes
Ctruncate Introduced DNA/RNA reference curve; uses flat prior on request, or when have tNCS or twinning
Othercell Various bug fixes
Pointless Correction for XDS input
Scala Corrected output for C1/2
PISA, QtPISA Stability fixes and generation of Remark 350 in no-complex situations
PDBCur Finish gracefully, rather than terminate, when atom selection is empty
PDB_Merge Various bug fixes
Xia2 Correction to Ctruncate wrapper
Aimless Various bug fixes
Ctruncate Introduced DNA/RNA reference curve; uses flat prior on request, or when have tNCS or twinning
Othercell Various bug fixes
Pointless Correction for XDS input
Scala Corrected output for C1/2
PISA, QtPISA Stability fixes and generation of Remark 350 in no-complex situations
PDBCur Finish gracefully, rather than terminate, when atom selection is empty
PDB_Merge Various bug fixes
Xia2 Correction to Ctruncate wrapper
Aimless Various bug fixes
Ctruncate Introduced DNA/RNA reference curve; uses flat prior on request, or when have tNCS or twinning
Othercell Various bug fixes
Pointless Correction for XDS input
Scala Corrected output for C1/2
PISA, QtPISA Stability fixes and generation of Remark 350 in no-complex situations
PDBCur Finish gracefully, rather than terminate, when atom selection is empty
PDB_Merge Various bug fixes
Xia2 Correction to Ctruncate wrapper
Ctruncate Introduced DNA/RNA reference curve; uses flat prior on request, or when have tNCS or twinning
Othercell Various bug fixes
PISA, QtPISA Stability fixes and generation of Remark 350 in no-complex situations
PDBCur Finish gracefully, rather than terminate, when atom selection is empty
PDB_Merge Various bug fixes
Xia2 Correction to Ctruncate wrapper
phaser.ensembler Corrected path to syminfo.lib
6.3.0-01310.01.13 molrep: Significantly more accurate packing function implemented
pisa: Now reports on monomeric properties in a no-complex situations
JLigand: Compounds derived from smile strings are now automatically regularised
QtRView: Improved performance on large log-files, added inverse resolution scale in graphs, coot and ccp4mg configuration is now optionally imported from ccp4i
molrep: Significantly more accurate packing function implemented
pisa: Now reports on monomeric properties in a no-complex situations
JLigand: Compounds derived from smile strings are now automatically regularised
QtRView: Improved performance on large log-files, added inverse resolution scale in graphs, coot and ccp4mg configuration is now optionally imported from ccp4i
Ensembler
Sculptor
: Permissions fixed for enabling users other than root to use these applications
molrep: Significantly more accurate packing function implemented
pisa: Now reports on monomeric properties in a no-complex situations
JLigand: Compounds derived from smile strings are now automatically regularised
QtRView: Improved performance on large log-files, added inverse resolution scale in graphs, coot and ccp4mg configuration is now optionally imported from ccp4i
Ensembler
Sculptor
: Permissions fixed for enabling users other than root to use these applications
molrep: Significantly more accurate packing function implemented
pisa: Now reports on monomeric properties in a no-complex situations
JLigand: Compounds derived from smile strings are now automatically regularised
QtRView: Improved performance on large log-files, added inverse resolution scale in graphs, coot and ccp4mg configuration is now optionally imported from ccp4i
Crank: Fix for preventing terminal windows from popping up
CProdrg: HETATM notations synchronised with refmac
Pointless
Aimless
: Now able to handle twice bigger datasets
Scala: Corrections to plot titles
Phaser: Added missing cctbx library files
6.3.0-01220.12.12 QtRView: Stability fixes and improved user experience of dynamically changing report pages
CCP4 Update: Technical modifications to ccp4-6.3.0 in order to complete the changes introduced in update No 11
QtRView: Stability fixes and improved user experience of dynamically changing report pages
CCP4 Update: Technical modifications to ccp4-6.3.0 in order to complete the changes introduced in update No 11
QtRView: Stability fixes and improved user experience of dynamically changing report pages
CCP4 Update: Technical modifications to ccp4-6.3.0 in order to complete the changes introduced in update No 11
QtRView: Stability fixes and improved user experience of dynamically changing report pages
CCP4 Update: Technical modifications to ccp4-6.3.0 in order to complete the changes introduced in update No 11
Crank: Bug fixes in mapro.exe module
6.3.0-01114.12.12 Aimless: Improvements to the CCP4i interface to Aimless
MrBUMP: Some changes to the output for compatibility with QtRView
Xia2: Updated to version 0.3.5.0
Areaimol: Fix for already allocated array problem
CCP4 update: Modifications required for integration in the next CCP4 Release
Aimless: Improvements to the CCP4i interface to Aimless
MrBUMP: Some changes to the output for compatibility with QtRView
Xia2: Updated to version 0.3.5.0
Areaimol: Fix for already allocated array problem
CCP4 update: Modifications required for integration in the next CCP4 Release
Aimless: Improvements to the CCP4i interface to Aimless
MrBUMP: Some changes to the output for compatibility with QtRView
Xia2: Updated to version 0.3.5.0
Areaimol: Fix for already allocated array problem
CCP4 update: Modifications required for integration in the next CCP4 Release
Aimless: Improvements to the CCP4i interface to Aimless
MrBUMP: Some changes to the output for compatibility with QtRView
Xia2: Updated to version 0.3.5.0
Areaimol: Fix for already allocated array problem
sortmtz: Fixes makng big data sets treatable
CCP4 update: Fixes for windows security issues and modifications required for integration in the next CCP4 Release
6.3.0-01010.12.12 QtRView: A new results viewer with graphs and launchers for Coot, CCP4MG and ViewHKL
Nautilus: Added missing template pdb-file
Hgen: Bug fix in task interface
Acorn: Bug fix in task interface
Crank: Bug fix in ctruncate plugin
Monomer Library: Several entries manually curated
QtRView: A new results viewer with graphs and launchers for Coot, CCP4MG and ViewHKL
Nautilus: Added missing template pdb-file
Hgen: Bug fix in task interface
Acorn: Bug fix in task interface
Crank: Bug fix in ctruncate plugin
Monomer Library: Several entries manually curated
QtRView: A new results viewer with graphs and launchers for Coot, CCP4MG and ViewHKL
Nautilus: Added missing template pdb-file
Hgen: Bug fix in task interface
Acorn: Bug fix in task interface
Crank: Bug fix in ctruncate plugin
Monomer Library: Several entries manually curated
QtRView: A new results viewer with graphs and launchers for Coot, CCP4MG and ViewHKL
Nautilus: Added missing template pdb-file
Hgen: Bug fix in task interface
Acorn: Bug fix in task interface
Crank: Bug fix in ctruncate plugin
Monomer Library: Several entries manually curated
6.3.0-00912.11.12 Refmac: Some minor bug fixes
Gesamt: File names now included in PDB screening output
Refmac: Some minor bug fixes
Gesamt: File names now included in PDB screening output
Refmac: Some minor bug fixes
Gesamt: File names now included in PDB screening output
Refmac: Some minor bug fixes
Gesamt: File names now included in PDB screening output
6.3.0-00819.10.12 Pointless: Fixed Choose Spacegroup option for non-standard settings, e.g. P21 2 21
Arp/Warp: Arp/Warp task interfaces preinstalled; will become active on installation of Arp/Warp. This fixes problem with overwriting modules.def file by other updates.
Zanuda: Made consistent with MSE atoms defined as HETATM in pdb-files
Pointless: Fixed Choose Spacegroup option for non-standard settings, e.g. P21 2 21
Arp/Warp: Arp/Warp task interfaces preinstalled; will become active on installation of Arp/Warp. This fixes problem with overwriting modules.def file by other updates.
Zanuda: Made consistent with MSE atoms defined as HETATM in pdb-files
Pointless: Fixed Choose Spacegroup option for non-standard settings, e.g. P21 2 21
Arp/Warp: Arp/Warp task interfaces preinstalled; will become active on installation of Arp/Warp. This fixes problem with overwriting modules.def file by other updates.
Zanuda: Made consistent with MSE atoms defined as HETATM in pdb-files
Phaser: Added DLL files missing in the previous update
Pointless: Fixed Choose Spacegroup option for non-standard settings, e.g. P21 2 21
Zanuda: Made consistent with MSE atoms defined as HETATM in pdb-files
6.3.0-00710.10.12 PHASER: Update to phaser version 2.5.2
ensembler interface: New interface for phaser.ensembler
Diffraction Image Libraries: Bug fixes to fix issues with displaying of pilatus images
ctruncate: Bug fix for issue with the computation of first principles twinning operators for some spacegroups (H3,H32)
PHASER: Update to phaser version 2.5.2
ensembler interface: New interface for phaser.ensembler
Diffraction Image Libraries: Bug fixes to fix issues with displaying of pilatus images
ctruncate: Bug fix for issue with the computation of first principles twinning operators for some spacegroups (H3,H32)
PHASER: Update to phaser version 2.5.2
ensembler interface: New interface for phaser.ensembler
Diffraction Image Libraries: Bug fixes to fix issues with displaying of pilatus images
ctruncate: Bug fix for issue with the computation of first principles twinning operators for some spacegroups (H3,H32)
PHASER: Update to phaser version 2.5.2
ctruncate: Bug fix for issue with the computation of first principles twinning operators for some spacegroups (H3,H32)
6.3.0-00605.10.12 MrBUMP: Model building options added
AMPLE: Bug fixes and expanded interface
PISA: New QT interface
ccp4i: New AMPLE and MrBUMP interfaces, QT-PISA launcher and bug fixes
DiffractionImage: corrections to reading of pilatus mini-cbf
tlsextract: correction of output format which broke parsing of output
MrBUMP: Model building options added
AMPLE: Bug fixes and expanded interface
PISA: New QT interface
ccp4i: New AMPLE and MrBUMP interfaces, QT-PISA launcher and bug fixes
DiffractionImage: corrections to reading of pilatus mini-cbf
tlsextract: correction of output format which broke parsing of output
MrBUMP: Model building options added
AMPLE: Bug fixes and expanded interface
PISA: New QT interface
ccp4i: New AMPLE and MrBUMP interfaces, QT-PISA launcher and bug fixes
DiffractionImage: corrections to reading of pilatus mini-cbf
tlsextract: correction of output format which broke parsing of output
MrBUMP: Model building options added
PISA: New QT interface
ccp4i: New MrBUMP interface, QT-PISA launcher and bug fixes
Crank: various bug fixes
6.3.0-00521.09.12Cumulative update for:
areaimol: fixed segmentation fault due to a bug in dynamic memory allocation
cprodrg: HETATM notations synchronised with refmac
ccp4i: fixes in refmac harvesting
Cumulative update for:
areaimol: fixed segmentation fault due to a bug in dynamic memory allocation
cprodrg: HETATM notations synchronised with refmac
ccp4i: fixes in refmac harvesting
Cumulative update for:
areaimol: fixed segmentation fault due to a bug in dynamic memory allocation
cprodrg: HETATM notations synchronised with refmac
ccp4i: fixes in refmac harvesting
Cumulative update for:
areaimol: fixed segmentation fault due to a bug in dynamic memory allocation
cprodrg: HETATM notations synchronised with refmac
ccp4i: added kill job functionality and fixes in refmac harvesting
6.3.0-00414.09.12Cumulative update for:
ViewHKL: a) added confidence measure for space group b) corrected scales for image size, reflection intensity and contrast
Updater: a) added permissions change functionality b) fixed bugs in proxy support
Cumulative update for:
ViewHKL: a) added confidence measure for space group b) corrected scales for image size, reflection intensity and contrast
Updater: a) added permissions change functionality b) fixed bugs in proxy support
Cumulative update for:
ViewHKL: a) added confidence measure for space group b) corrected scales for image size, reflection intensity and contrast
Updater: a) added permissions change functionality b) fixed bugs in proxy support
Cumulative update for:
Scala: fixed bug which was causing presence of NaNs and wrong numbers in standard output
ViewHKL: a) added confidence measure for space group b) corrected scales for image size, reflection intensity and contrast
Updater: a) added permissions change functionality b) fixed bugs in proxy support
6.3.0-00305.09.12Cumulative update for:

CTruncate module: bug fixes
ShelX C/D/E task interface: introduced the autotracing option
Zanuda module and task interface: bug fixes
Cumulative update for:

CTruncate module: bug fixes
ShelX C/D/E task interface: introduced the autotracing option
Zanuda module and task interface: bug fixes
Cumulative update for:

CTruncate module: bug fixes
ShelX C/D/E task interface: introduced the autotracing option
Zanuda module and task interface: bug fixes
Cumulative update for:

CTruncate module: bug fixes
ShelX C/D/E task interface: introduced the autotracing option
Zanuda module and task interface: bug fixes
6.3.0-00205.09.12Technical modifications to ccp4-6.3.0 in order to complete the installation of update functionalitiesTechnical modifications to ccp4-6.3.0 in order to complete the installation of update functionalitiesTechnical modifications to ccp4-6.3.0 in order to complete the installation of update functionalitiesTechnical modifications to ccp4-6.3.0 in order to complete the installation of update functionalities
6.3.0-00105.09.12Modification of ccp4i to integrate update functionalities. You will need to restart ccp4i after the update for changes to take an effect.Modification of ccp4i to integrate update functionalities. You will need to restart ccp4i after the update for changes to take an effect.Modification of ccp4i to integrate update functionalities. You will need to restart ccp4i after the update for changes to take an effect.Modification of ccp4i to integrate update functionalities. You will need to restart ccp4i after the update for changes to take an effect.

Reporting bugs

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