Dm Error In Label Assignments In Labin

Note that there are several independent documents linked here covering different platforms, different versions of CCP4 and different components of CCP4. If you can't find your problem here, please email us.

A list of more general version-unspecific problems can be found on the General Problems Page as well as descriptions of various operating system-specific eccentricities.

A list of general and version-independent problems with CCP4i can be found here:

Note that an issue exists with WinCoot 0.6.2, previously distributed by CCP4. In this version the program findwaters crashes midway through its run. This program can be solved by replacing findwaters-real.exe in WinCoot\bin with the version available from Bernhard's site

WinCoot 0.6.2.1 is unaffected by this problem.

  • Phaser MR: Fails to carry out search in alternative selected space group
    Date : 15/08/2012
    CCP4 Version : v6.3.0
    System : all
    Level : Minor
    Status : workaround, fix will come later
    Bugzilla number : #4884

    Phaser fails to search in the selected alternative spacegroup when one alternative SG is selected.

    The workaround is to either modify the space group in the MTZ header or select more than one alternative spacegroup to search in. Fixed executables and source code will be available in the near future.

    More details are available from the Phaser wiki bugs page.


  • Libcheck: processed SMILES string gets garbled in Coot or JLigand
    Date : 16/08/2012
    CCP4 Version : v6.3.0
    System : all
    Level : Minor
    Status : workaround, fix will come later
    Bugzilla number : #4886

    Libcheck produces a garbled model for a SMILES string in certain cases. This will be observed in any program that calls libcheck to generate restraints information such as Coot or Jligand.

    The current workaround is to replace the CCP4 6.3.0 version of libcheck in the $CCP4/bin directory with the version from the previous CCP4 release (6.2.0). These can be downloaded for Linux, MAC and Window from here:

    libcheck (Linux)
    libcheck (Mac OSX)
    libcheck.exe (Windows)

    An fixed version for the current libcheck will be available in the near future.

    (Thanks to Hari Jayaram)


  • AMPLE: Fails with error message about missing argparse module
    Date : 16/08/2012
    CCP4 Version : v6.3.0
    System : Linux
    Level : Major
    Status : Fixed
    Bugzilla number : #4887

    The beta version of AMPLE distributed with the original CCP4 6.3.0 (downloaded from CCP4 site before 15/08/12) has several minor bugs. It may complain of a missing argparse module.

    An updated tar-ball is available (below) which should be extracted from the top level CCP4 directory ($CCP4). It will replace older AMPLE files and correct the problems.

    The updated tar-ball is available from here: ample-update.tar.gz


  • Areaimol: Fails with segmentation fault or gives NAN or Infinity values
    Date : 17/08/2012
    CCP4 Version : v6.3.0
    System : Linux & Windows
    Level : Minor
    Status : Fixed
    Bugzilla number : #4888

    Areaimol, when compiled with certain compilers (e.g. gcc 4.4.3), will give a segmentation fault or give garbage values for its calculations (NAN's and Infinities). This was caused by a memory leak in the code.

    The source code has been fixed and the memory leak removed. Updated binaries for Linux systems (32 & 64 bit) and Windows are available below.

    areaimol (Linux 32 bit)
    areaimol (Linux 64 bit)
    areaimol.exe (Windows)

    (Thanks to Phil Evans)


  • cprodrg: Fails with refmac error
    Date : 14/09/2012
    CCP4 Version : v6.3.0
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #4901

    cprodrg, when run on pdb files with HETATM records fails after running refmac

    The source code has been fixed. Updated binaries for Linux systems (32 & 64 bit) and OS X are available below. For source code compilation, the c_refmac.f file should be replaced by the new one.

    cprodrg (Linux 32 bit)
    cprodrg (Linux 64 bit)
    cprodrg (OS X)
    Prodrg/c_refmac.f

    (Thanks to Andrew Sharff)


  • high symmetry point groups ISYM scrambling
    Date : 29/07/2011
    CCP4 Version : v6.2.0
    System : all
    Level : Major
    Status : fix and file updates
    Bugzilla number : #4599

    ==== Summary

    There is a serious error in all the 1.5.x versions of Pointless for certain cases, fixed now in version 1.6.1 available now from our ftp site. The wrong 1.5.x versions have been distributed by CCP4 in releases 6.1.24 and the recent 6.2.0, but earlier CCP4 releases (6.1.13 and before) contained earlier versions of Pointless (eg 1.4.x versions) which do not suffer from this bug. However I know that people have installed 1.5.x versions from our ftp site.

    I would like to apologise for problems caused by this error mea culpa
    Phil Evans

    === Corrected versions

    Available from ccp4 ftp for linux, os x and windows. Also a source can be used in ccp4-6.2.0/src.

    OR

    ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre

    • pointless-1.6.1.linux linux executable
    • pointless-1.6.1.osx10.6 osx 10.6 executable
    • pointless-1.6.1.tar.gz source
    • pointless.html doc

    These replace the distributed versions

    === What cases does the bug affect?

    The bug may scramble the order of symmetry operators relative to the ISYM flags on each observation (see below, technicalities), leading to an incorrect reconstruction of the original hkl indices in Scala or Aimless. This happens for MTZ input files (usually from Mosflm) integrated is the highest point group in higher symmetry lattices, specifically tetragonal 422, hexagonal 622, rhombohedral R32 and cubic 432, when the output file is also in the same point group. In these cases, the output file will be wrong even if Pointless is just copying from input to output ("-c" or COPY options)

    The bug does NOT affect:

    1. lower symmetry lattices (triclinic, monoclinic, orthorhombic)
    2. data input or output in lower than maximum point group symmetry within the same Laue class (eg 4, 3, 321, 23, R3)
    3. XDS or other non-MTZ input

    === How serious is it?

    Files with scrambled symmetry operators will lead to wrong reconstruction of the original indices which are used in Scala or Aimless to generate beam directions for the SECONDARY absorption correction. Thus the error will have the biggest effect on long wavelength data with substantial absorption, and have much less effect on typical short wavelength data. High multiplicity will also tend to average out the errors.

    === Technicalities

    Unmerged MTZ files store for each observation the hkl indices reduced to the asymmetric unit and a flag ISYM which is the index into the list of space group symmetry operators stored in the file. This information can then be used to reconstruct the original hkl indices measured. This bug caused to order of the symmetry operators to be changed without changing the ISYM flags, leading to a wrong reconstruction of original hkl in Scala/Aimless, and hence wrong secondary beam directions for the absorption correction.

    (Thanks to Phil Evans)


  • Molrep: input fixed model mode failure
    Date : 08/08/2011
    CCP4 Version : v6.2.0
    System : all
    Level : Minor
    Status : fix and file updates
    Bugzilla number : #4610

    The input fixed model mode of molrep fails with the message (linux version)

    Fortran runtime error: End of record

    For binary distributions replace the molrep binary with the appropriate file for linux, os x or windows. For source builds replace $CCP4/src/molrep_/molrep.f with the updated file.


  • POINTLESS: XDS XSCALE option missets orientation matrix
    Date : 06/09/2011
    CCP4 Version : v6.2.0 pre 20/09/2011, pointless pre 1.6.2
    System : all
    Level : Minor
    Status : fix and file updates
    Bugzilla number : #4636

    The XDS XSCALE output from pointless causes problems in reindexas used by xia2.

    Available from ccp4 ftp for linux, os x. Also a source can be used in ccp4-6.2.0/src.

    OR

    ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre

    • pointless-1.6.5.linux linux executable
    • pointless-1.6.4.osx10.6 osx 10.6 executable
    • pointless-1.6.5.tar.gz source
    • pointless.html doc

    These replace the distributed versions


  • Phaser: 32 bit binary occasionally aborts on 64 bit Linux
    Date : 19/10/2011
    CCP4 Version : v6.2.0 pre 19/10/2011
    System : Linux binary distribution
    Level : Minor
    Status : fix and file updates
    Bugzilla number : #4637

    Certain jobs fail occasionally reporting when the distributed 32 bit phaser binary is run under 64 bit Linux.

    A fixed version is available from the ftp site. This version also replaces the distributed binary in automated downloads from this point onwards.


  • Sfcheck: failure with a large mtz-file
    Date : 11/12/2011
    CCP4 Version : v6.2.0
    System : all
    Level : Minor
    Status : fix and file updates
    Bugzilla number : #4709

    Sfcheck fails for a large mtz-file with the message (mac version)

    forrtl: severe (174): SIGSEGV, segmentation fault occurred

    For binary distributions replace the sfcheck binary with the appropriate file for linux, os x or windows. For source builds replace $CCP4/src/sfcheck_ with the updated directory.


  • Including file with known HA sites in autoSHARP doesn't work correctly
    Date : 23/02/2009
    CCP4 Version : 6.1.1
    System : all
    Level : minor
    Status : fixed
    Bugzilla number : n/a

    The procedure for including a file with known HA sites needs to be modified to take into account whether one is using SAD/MAD or SIR/MIR.

    This can be done by using three updated ccp4i files:

    • autoSHARP.tcl - replace the version in $CCP4/ccp4i/tasks (or $CCP4/share/ccp4i/tasks)
    • autoSHARP.def - replace the version in $CCP4/ccp4i/tasks (or $CCP4/share/ccp4i/tasks)
    • autoSHARP.script - replace the version in $CCP4/ccp4i/scripts (or $CCP4/share/ccp4i/scripts)

    (Thanks to Clemens Vonrhein)


  • Sketcher crashes when attempting to open periodic table
    Date : 23/02/2009
    CCP4 Version : 6.1.1
    System : all
    Level : minor
    Status : fixed
    Bugzilla number : n/a

    This replacement file corrects the problem using a updated ccp4i file:

    • sketch_table.tcl - replace the version in $CCP4/ccp4i/sketch (or $CCP4/share/ccp4i/sketch)

    (Thanks to Liz Potterton)


  • Mapslicer libccp4map.so: undefined symbol: ccp4_file_itemsize
    Date : 02/03/2009
    CCP4 Version : 6.1.1
    System : all
    Level : minor
    Status : workarounds
    Bugzilla number : 3711

    mapslicer fails to launch in ccp4 linux binaries, and when built using the default build.

    This is due to missing symbols from the ccp4c library. Several workarounds exist

    • All binaries - remove libccp4map.so. mapslicer will use the static ccp4mapwish instead
    • Prebuilt linux binary - replace libccp4map.so with an updated version
    • Source code build on linux - reconfigure and rebuild using this updated configure

  • Amplitude based twin refinement option not being passed to program
    Date : 02/03/2009
    CCP4 Version : 6.1.1
    System : all
    Level : minor
    Status : workaround
    Bugzilla number : 3713

    When selecting amplitude based twin refinement in ccp4i, the option is not passed to refmac5.

    This replacement file corrects the problem using an updated ccp4i file

    • refmac5.com - replace the version in $CCP4/ccp4i/templates (or $CCP4/share/ccp4i/templates)

    (Thanks to Raj Pannu)


  • Old Refmac jobs cannot be rerun
    Date : 06/03/2009
    CCP4 Version : 6.1.1
    System : all
    Level : minor
    Status : workaround
    Bugzilla number : 3690

    Attempting to rerun an old Refmac job results in the job getting stuck in the 'STARTING' state. On non-Windows platforms there is also an error message:

    "ATOM(0)": variable isn't array ...

    This is because changes have been made to the Refmac interface in CCP4-6.1.1 which are not backwardly compatible. This replacement file corrects the problem using an updated ccp4i file

    • refmac5.tcl - replace the version in $CCP4/ccp4i/tasks (or $CCP4/share/ccp4i/tasks)

  • scalepack2mtz (and dtrek2mtz) interfaces do not pass DNAME, XNAME to program
    Date : 08/03/2009
    CCP4 Version : 6.1.1 and before
    System : all
    Level : minor
    Status : workaround and fix
    Bugzilla number : 3721

    Attempting to define the dataset and crystal names through the scalepack2mtz interface, or import_scaled interface does not work. A workaround and fix using replacement files is given

    • Either: use Run and View Com to add the correct form name project
    • Or: scalepack2mtz.com - replace the version in $CCP4/ccp4i/templates (or $CCP4/share/ccp4i/templates)
    • dtrek2mtz.com - replace the version in $CCP4/ccp4i/templates (or $CCP4/share/ccp4i/templates)
    • pname2.com - add to $CCP4/ccp4i/templates (or $CCP4/share/ccp4i/templates)

  • Ctruncate failure when run as part of the Import Scaled task
    Date : 11/03/2009 (revised 23/03/2009)
    CCP4 Version : 6.1.1
    System : all
    Level : minor
    Status : fixed
    Bugzilla number : 3722, 3789

    If the Import Scaled task is run with the "Ctruncate" and "Use dataset name as identifier to append to column labels" options selected, the job will fail with error message

    can't read "dataset_name": no such variable

    There is an updated ccp4i file (further updated on 23/03/2009) which should fix this problem:

    (Thanks to Matsuura Takanori and Nick Bauer)


  • imosflm exits with invalid command iwidgets::tabnotebook
    Date : 24/04/2009
    CCP4 Version : 6.1.1 using tcltk++
    System : FC10 and perhaps others
    Level : minor
    Status : workaround
    Bugzilla number : 3798

    Running imosflm exits with

    $ imosflm MOSDIR is Error in startup script: invalid command name "iwidgets::tabnotebook" while executing "iwidgets::tabnotebook $itk_interior.f.tabs -tabpos n -background "#dcdcdc" -tabbackground "#a9a9a9" -foreground "black" -tabforeground "black" ..."

    This is due to tclIndex not being copied from tcltk++/iwidgets4.0.1/generic to the <install loc>/lib/iwidgets4.0.1/scripts during the build-tcl-tk++.sh process. The solution is to manually copy the file.


  • FFT routines fail on Itanium with Intel 9.1 compilers
    Date : 24/11/2006
    CCP4 Version : 6.0.2
    System : Itanium ia64
    Level : Minor
    Status : Fixed
    Bugzilla number : #1503

    Compilation with a default Fortran optimisation level of -O2 causes programs which use Fast Fourier Transforms to fail, because the compiler does not perform integer division correctly. The fix is to reduce optimisation to -O1.

    The fix is available as a patch configure-r1.372.2.18-r1.372.2.19.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches) to $CCP4/configure.

    Note that compilation using Intel 9.0 compilers fails entirely, apparently because of missing symbols in the compiler's C library.

  • Refmac5 compilation fails on gfortran compilation
    Date : 19/02/2007
    CCP4 Version : 6.0.2
    System : gfortran
    Level : fatal
    Status : fixed
    Bugzilla number : n/a

    Compilation of Refmac5.2 with gfortran 4.1.1 (and possibly other versions?) fails with:

    ccp4e.log:105:make[1]: *** [make_unix_ccp4.o] Error 1 ccp4e.log:106:make: *** [srcdir] Error 2 ccp4e.log:115:make[1]: *** [make_unix_ccp4.o] Error 1

    The fix is to change IDATE into UIDATE because gfortran 4.1.1 IDATE specifications have changed, UIDATE is a ccp4 routine which does not change:

    .../ccp4/src/refmac5_$ cvs diff -r1.10 -r1.11 make_unix_ccp4.f diff -r1.10 -r1.11 100c100 < CALL IDATE(IMON,IDAY,IYR) --- > CALL UIDATE(IMON,IDAY,IYR)
  • Problems with output SHELX option of mtz2various
    Date : 06/03/2007
    CCP4 Version : 6.0.2
    System : all
    Status : fixed
    Bugzilla number : #2189

    MTZ2VARIOUS used to output a header to the SHELX file. The idea was that this was a template for the required foo.ins file. However, this is not convenient and has been removed. Reflections in the free-R set were also flagged with "FREE" which can no longer be read by SHELX, so this has been removed. Output from the FSQUARED option was automatically scaled to avoid format overflow. This has now been applied to intensity output as well. Finally, it was possible to use "LABIN I=I SIGI=SIGI" which is better than the FSQUARED option, but this was erroneously flagged as HKLF 3 output. This is now fixed.

    Updated files are available:

    (Thanks to Ian Tickle)

  • Cannot find the "configure" subdirectory after automatic installation of CCP4
    Date : 07/03/2007
    CCP4 Version : 6.0.2
    System : all UNIX/Linux
    Status : fixed
    Bugzilla number : #2184

    There is an error in the section of the CCP4 installation documentation dealing with the automated installer script for UNIX and Linux platforms, e.g. at http://www.ccp4.ac.uk/dist/INSTALL.html#install_sh.

    The documentation refers to a "configure" subdirectory that should be created as part of the installation process, and which should contain the setup files (e.g. ccp4.setup) for the installation.

    However this information is no longer correct. The revised text should read:

    The script will also generate a setup-scripts subdirectory that contains set-up files for the various packages (i.e. ccp4.setup for the core suite and programs, and ccp4-others.setup for CCP4mg and Coot) for Bourne/Bash shell (in the sh subdirectory of setup-scripts) and C-shell (in the csh subdirectory). To start using the software you should only need to source the appropriate set-up files for your shell.

    The installation documentation has been updated for future releases of the suite.

    (Thanks to Susumu Ichiyama)

  • Linking stage fails with undefined reference to `ccp4_fflush_stdout_'
    Date : 05/06/2007
    CCP4 Version : 6.0.2 with update to phaser 2.1.3
    System : all UNIX/Linux
    Status : fixed
    Bugzilla number : #3020

    The phaser 2.1.3 update includes a updated ccp4_general_f.c which calls ccp4_flush_stdout which should be in unix.m4. A replacement unix.m4 is available.

  • mtz2various scalepack output broken
    Date : 14/07/08
    CCP4 Version : 6.0.2
    System : All except Windows
    Level : Minor
    Status : Fixed
    Bugzilla number : #3162

    The output from mtz2various in scalepack format was incorrect for pairs where I- was measured but I+ was not. Also fixes lack of meaningful output when intensities are read rather than structure factor amplitudes. mtz2various.f-r1.124.2.3-r1.136.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches) to $CCP4/src/mtz2various.f and remaking mtz2various.

    (Thanks to Pete Dunten)

  • Topp can't find input files
    Date : 23/11/06
    CCP4 Version : 6.0.2
    System : All except Windows
    Level : Minor
    Status : Fixed
    Bugzilla number : #1936

    Topp claims it cannot find the input files corresponding to keywords MOL1 and MOL2, even though the files exist.

    This can be fixed by applying the patch topp.f-r1.16.2.5-r1.16.2.6.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches) to $CCP4/src/topp_/topp.f and remaking topp.

  • Fix for output formatting in Scala
    Date : 29/11/06
    CCP4 Version : 6.0.2
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #1939

    An extra space has been added to the output line for the analysis against resolution, Mn(I/sd) from Scala to allow for values of I/sigma equal to or greater than 100. This patch is particularly important for users of XIA.

    This can be fixed by applying the patch scala.f-r1.101.2.3-r1.101.2.4.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches) to $CCP4/src/scala_/scala.f and remaking scala.

    There is also an updated Scala windows executable available from here: scala.exe

    (Thanks to Graeme Winter)

  • Fix for HKLIN input order error in Polarrfn
    Date : 15/1/07
    CCP4 Version : 6.0.2
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #2045

    Polarrfn is sensitive to the ordering of its input HKLIN files. If the order is one way the program works fine but if the files are reversed the program exits prematurely with an end of file error.

    This can be fixed by applying the patch polarrfn.f-r1.45.2.1-r1.45.2.2.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches) to $CCP4/src/polarrfn.f and remaking polarrfn.

    (Thanks to Pete Dunten)

  • Amore output corrupt if more than 9 molecules in asu
    Date : 18/1/07
    CCP4 Version : 6.0.2
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #2047

    The number of fixed translation solutions allowed as input to Amore was limited to 8. Consequently one was restricted to finding no more than 9 molecules in the asu (8 fixed + 1 new). No error message was given if this limit was exceeded. Instead the output Euler angles and fractional translations became corrupted, due to array boundaries being exceeded.

    The limit has been increased from 8 to 64, and an error message is printed if the new limit is exceeded. The translation function output has been changed slightly to allow for two digit labels. The changes are available as a patch: amore.f-r1.115-r1.116.diff.

    Note added 26/11/07: If running through ccp4i, the following patch should also be installed: amore_utils.tcl-r1.14-r1.15.diff.

    (Thanks to Adrian Lapthorn)

  • cmakereference requires compressed files
    Date : 23/1/07
    CCP4 Version : 6.0.1 and 6.0.2
    System : All
    Level : Minor
    Status : Informational
    Bugzilla number : #2074

    The version of cmakereference distributed with CCP4 6.0.1/2 requires compressed .ent.Z files. Sometimes an uncompressed file may be downloaded from an archive site. This should be compressed using compress before using cmakereference.

    Note: the supplied reference data in $CLIBD/reference_structures should be suitable in all but the most exotic cases.

  • Format error in bp3 loggraph output
    Date : 13/02/07
    CCP4 Version : 6.0.2
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #2143

    There are some minor format errors in the Isomorphism Correlation table output by bp3, which cause loggraph and xloggraph to fail when used to view this data.

    These can be corrected by use of the patch crystal.C-r1.5-r1.6.diff.

    (Thanks to Graeme Winter)

  • SORTMTZ fails with "Too many records" e.g. when running the SCALA task
    Date : 07/03/07
    CCP4 Version : 6.0.2 and earlier
    System : Windows
    Level : Minor
    Status : Fixed
    Bugzilla number : #1625

    When running SORTMTZ for example as part of the "Scale and Merge Intensities" (SCALA) task, the program may fail with the message "Too many records".

    This has been reported when the MTZ file provided as input is very large (the file causing the current problem contained of the order of 2.5 million reflections in 70 batches).

    This has been reported on Windows systems, where there may be similar problems with CAD, SCALEIT and SCALA itself. The fix for Windows users is to obtain the compressed .zip file from the CCP4 FTP server:

    This file contains new versions of , and , which should be put into the "bin" directory within your CCP4 installation to replace the distributed versions.

    (Thanks to Richard Strange, Graeme Winter and Francois Remacle)

  • CIF output from MTZ2VARIOUS has incorrect date format
    Date : 08/03/07
    CCP4 Version : 6.0.2 and earlier
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #2195

    The cif file created by mtz2various contains the "_audit.creation_date" item in "yyyy-dd-mm" format. It should actually be "yyyy-mm-dd" according, to the mmCIF dictionary:

    The following patch to corrects the writing of the date information:

    (Thanks to Takaaki Fukami)

  • Problem in aniso_eigens in Refmac5
    Date : 22/03/07
    CCP4 Version : 6.0.2
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #2157

    There is a small bug that crops up on some occasions with the 6.0.2 version of Refmac5. One of the eigenvector calculations encounters an error and causes the program to terminate with the error message "Problem in aniso_eigens #", where # is some integer value. The latest version of refmac available from the York YSBL site fixes this and is available from:

    http://www.ysbl.york.ac.uk/~garib/refmac/latest_refmac.html.
  • Assigning I input problem with FFT
    Date : 06/05/07
    CCP4 Version : 6.0.2
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #2339

    The option of inputting already squared values (e.g. F2OR/E2OR from ecalc) into FFT, by assigning it to I instead of F1, causes FFT to write out some incorrect information. It also causes it to not switch to the correct Patterson space-group. This can be corrected by applying the following patch to fft.f:

    fft.f-r1.98-r1.100.diff.

    (Thanks to Clemens Vonrhein)

  • RSTATS failure in autoSHARP script
    Date : 31/05/07
    CCP4 Version : 6.0.2 and earlier
    System : All
    Level : Normal
    Status : Fixed
    Bugzilla number : #2421

    Running rstats from the autoSHARP script may result in divide by zero errors. This is because the autoSHARP script only outputs a subset of the input mtzfile columns into the output mtzfile which "corrupts" the internal representation of the mtzfile statistics. The fault lies entirely within rstats.

    This can be corrected by applying the following patch to rstats.f:

    rstats.f-r1.39-r1.40.diff.

    (Thanks to Markus Meier)

  • CAD clash between integer XNAME and Dataset ID
    Date : 08/06/07
    CCP4 Version : 6.0.2 and earlier
    System : All
    Level : Normal
    Status : Advisory
    Bugzilla number : #2447

    CAD may crash when an integer name is used as the crystal name (XNAME), otherwise, the behaviour is ill defined. It is strongly suggested that a pure integer not be used as the crystal name as this clashes with parsing within CAD, and possibly other CCP4 programs, with respect to the Dataset ID mechanism of accessing columns. A character should be contained within the XNAME.

  • Typo fix in BEAST_MPI
    Date : 20/07/07
    CCP4 Version : 6.0.2 and earlier
    System : All
    Level : Normal
    Status : Fixed
    Bugzilla number : #2474

    There is a typo error in one of the MPI_BCast calls in Beast_MPI. A patch to fix this can be found at the link below. (Note that beast is now deprecated from the suite and will not be included in releases after CCP4 6.1).

    beast_MPI.f-r1.1-r1.2.diff.

    (Thanks to Maier Timm)

  • Refmac truncates harvesting Project and Dataset names
    Date : 25/09/2007
    CCP4 Version : 6.0.2 and earlier
    System : All
    Level : minor
    Status : Fixed
    Bugzilla number : #2477 and 2609

    Refmac only allows ten characters each for the Project and Dataset names used for harvesting. Names longer than this will be truncated, which can lead to error messages when running from the ccp4i gui.

    The following patch increases the length allowed for these names to 64, in accordance with the MTZ file specification:

    rharvest.fh-r1.13-r1.14.diff.

    (Thanks to Ingo Korndoerfer and Herbert Klei)

  • "Run and edit com file" fails with an error
    Date : 11/12/2006
    CCP4 Version : 6.0.2 and earlier
    System : All
    Level : irritating
    Status : fixed
    Bugzilla number : #1955

    There is a bug with running a CCP4i job using the "Run and edit com file" option when the input file name is of the form foo.bar.mtz or similar (for example rnase.1.mtz). The job starts running but generates a window with an error message of the form:

    bad window path name ".edit_rnase"

    The job stops but its status remains as RUNNING. This will happen for any file with multiple "dots" in the name, regardless of extension.

    There are a couple of possible work-arounds:

    • Rename files so that they do not contain extra "dots" (e.g. rename foo.bar.mtz to foo_bar.mtz
    • Run the job using the "Run now" option only

    Alternatively, apply the following patch from the CCP4 ftp server to the file :

    To clean up a job that still appears to be running after this bug has occurred, select the job in question and then go to the Edit Job Data option under the menu of the same name (on the right-hand side of the main CCP4i window). You can then change the job status to FAILED.

    (Thanks to Randy Read)

  • Can't select Hendrickson-Lattman coefficients in Convert From MTZ task
    Date : 15/02/2007
    CCP4 Version : 6.0.2 and earlier
    System : All
    Level : inconvenient
    Status : fixed
    Bugzilla number : n/a

    H-L coefficients can be specified on the LABIN keyword of mtz2various when converting to X-PLOR/CNS format. However, this functionality is not available in the GUI.

    It is now. Fixed ccp4i files (also includes SHELX output fix):

    (Thanks to Bernie Santarsiero, Vineet Gaur)

  • Can't run Detwin from ccp4i on Windows
    Date : 04/04/2007
    CCP4 Version : 6.0.2
    System : Windows
    Level : minor
    Status : fixed
    Bugzilla number : #2252

    Attempting to start Detwin from ccp4i on windows gives an error message

    Error: wrong #args: should be "CreateTaskWindow arrayname title icon_name ?frame_list? args"

    This can be fixed by replacing the detwin.tcl in %CCP4%/ccp4i/tasks with a modified detwin.tcl.

  • Phaser job fails with "SYNTAX ERROR: Use ON or OFF"
    Date : 11/04/2007
    CCP4 Version : 6.0.2
    Status : fixed

    If "PDB file output" or "MTZ file output" are selected in the last folder "Additional parameters" then Phaser will fail with "SYNTAX ERROR: Use ON or OFF". This is because ccp4i adds quoting to ON or OFF which Phaser can't interpret.

    The quoting has been removed. A patch file is available at:

    Alternatively, the quotes can be removed on-the-fly with Run&View Com.

    (Thanks to Serge Cohen and Randy Read for alerting us.)

  • Multiple versions of control information in ccp4i com.tmp files
    Date : 31/05/2007
    CCP4 Version : 6.0.2
    System : All
    Level : minor, but difficult to spot
    Status : workaround
    Bugzilla number : #2418

    Under the circumstances that there is a pre-existing ...com.tmp file in $CCP4_SCR area with the same name as a generated file, ccp4i will append the input data to the pre-existing file. This may cause unexpected results. An example appending file for a unique job is shown:

    CELL 117.5058 125.8665 245.4758 90.0000 90.0000 90.0000 SYMMETRY 'P 21 21 21' LABOUT F=FUNI SIGF=SIGFUNI RESOLUTION 2.200 ## This script run with the command ########## # unique HKLOUT "/tmp/ccb/PROJECT1_25_3_mtz.tmp" ################################################ CELL 117.5058 125.8665 245.4758 90.0000 90.0000 90.0000 SYMMETRY 'I 21 21 21' LABOUT F=FUNI SIGF=SIGFUNI RESOLUTION 2.199 ## This script run with the command ########## # ################################################

    The solution is to rerun the job and/or delete the pre-existing ...com.tmp files.

  • Refmac (via ccp4i) gives the error: No file name for parameter MAPOUT1
    Date : 25/07/2007
    CCP4 Version : 6.0.2
    System : all
    Level : minor
    Status : fixed
    Bugzilla number : #1730

    Running Refmac via the ccp4i gui and asking it to generate weighted difference maps will result in the warning: "no file name for parameter MAPOUT1".

    A patched version of the file refmac5.tcl is available from here. Download this file and replace the old one in the folder $CCP4/ccp4i/tasks. See also Advice for Windows Users.

  • Issues running CCP4i using Tcl/Tk 8.5
    Date : 31/07/2008
    CCP4 Version : 6.0.2 and earlier
    System : all
    Level : minor
    Status : workaround
    Bugzilla number : #2914

    There are some known issues when running CCP4i using the latest version of Tcl/Tk (version 8.5), in particular the appearence of check buttons or toggle buttons.

    See the appropriate section of the CCP4i trouble-shooting pages for information.

  • anisoanl PDB output missing contents
    Date : 10/05/2006
    CCP4 Version : 6.0.1
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #1679

    the PDB file output from anisoanl is empty apart from the END line.

    This problem can be fixed by applying the following patch anisoanl.f-r1.22-r1.24.diff

  • sc at_excl keyword ignored until after radius assignment
    Date : 10/05/2006
    CCP4 Version : 6.0.1
    System : All
    Level : Minor
    Status : Fixed
    Bugzilla number : #1678

    You specify to exclude an atom using the at_excl keyword, but sc still fails if that atom is in the input coordinates and not in the SCRADII file.

    This is because the at_excl keyword is not processed until the input coordinates have been read and their radii looked up in the SCRADII file. This problem can be fixed by applying the following patches. sc.f-r1.9-r1.9.2.1.diff and setup.fh-r1.5-r1.5.2.1.diff

  • Chainsaw fails reading pdb file from Moleman2
    Date : 11/05/2006
    CCP4 Version : 6.0.1
    System : all
    Level : annoying
    Status : fixed
    Bugzilla number : #1677

    Chainsaw fails when modifying a C-terminal residue which contains atoms named OT1 and OT2. Such a file can be generated by using Moleman2 to split a pdb file containing NMR data into individual models.

    This can be fixed by applying the patch chainsaw.cpp-11May2006.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.1/patches) to $CCP4/src/mmdb_app_chainsaw.cpp and remaking chainsaw.

    (Thanks to Nick Keep)

  • Contact gives junk output when used with large pdb files
    Date : 12/06/2006
    CCP4 Version : 6.0.1
    System : all
    Level : annoying
    Status : fixed
    Bugzilla number : #1689

    Contact may give junk output when the input pdb file contains more than about 32000 atoms.

    This can be fixed by applying the patch contact.f-12June2006.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.1/patches) to $CCP4/src/contact.f and remaking contact.

    (Thanks to Andrew Leslie)

  • ACT stops when performing temperature factor analysis on a chain containing only one residue.
    Date : 6/07/2006
    CCP4 Version : 6.0.1
    System : all
    Level : annoying
    Status : fixed
    Bugzilla number : #1128

    Several problems have been encountered with the program ACT. The temperature factor analysis stops with error message

    ACT: MOMENT: n must be at least 2 if it encounters a chain containing only one residue.

    In addition, most HETAMs with three letter names are erroneously taken to be amino acids, causing them to be included in the Main chain/Side chain statistics.

    A number of array limit failures can also occur with pdb files containing a large number of atoms.

    Fixes have been incorporated in the patch act.f-6July2006.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.1/patches).

    (Thanks to Ketan Gajiwala)

  • Rotmat may give spurious hits
    Date : 17/07/2006
    CCP4 Version : 6.0.1
    System : all
    Level : minor
    Status : fixed
    Bugzilla number : #1737

    A bug in rotmat means that it may sometimes incorrectly claim to have detected a hit and the rotation angles may be incorrect.

    This can be fixed by applying the patch rotmat.f-17July2006.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.1/patches) to $CCP4/src/rotmat.f and remaking rotmat.

    (Thanks to Jean-Paul Declercq for spotting this bug and Eleanor Dodson for fixing it.)

  • Molrep fails when electron density map is used as model
    Date : 1/08/2006
    CCP4 Version : 6.0.1
    System : all
    Level : minor
    Status : fixed
    Bugzilla number : #1748

    When molrep is run using an electron density map as the model, the map may be read in incorrectly, due to an uninitialised variable in the code. This sometimes gives rise to the following error message

    ERROR: Rad_inertia of model = 0 (ROTDNS)

    The problem can be fixed by applying the patch molrep.f-r1.28-r1.28.2.1.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.1/patches) to $CCP4/src/molrep_/molrep.f and remaking molrep.

    Alternatively the latest version 9.4.05 of Molrep can be downloaded from York University.

    (Thanks to Joseph Ho for reporting this problem.)

  • Cad does not write history lines to output mtz file
    Date : 1/08/2006
    CCP4 Version : 6.0.1
    System : all
    Level : minor
    Status : fixed
    Bugzilla number : #1750

    In all versions of CCP4 later than 4.2.2, CAD fails to copy the history lines from the input mtz file(s) to the output mtz file. OMIT and MTZTONA4 suffer similar problems.

    Occasionally, memory faults can occur if there is a large number of history lines in the input.

    Fixes are available in the form of the following patches: cad.f-r1.70-r1.72.diff, omit.f-r1.12-r1.13.diff, mtztona4.f-r1.23-r1.24.diff.

  • polarrfn output contains NAN and map output corrupted
    Date : 10/08/2006
    CCP4 Version : 6.0.1
    System : all
    Level : minor
    Status : fixed
    Bugzilla number : #1753

    Polarrfn can exhibit a failure in which it appears to run correctly but the map contains only NaN.

    Weighted mean of map NaN Weighted rms 0.000

    This can be fixed by the simple one line change to polarrfn:

    149c149 < REAL ADATA(NLPRGI),COLRNG(2,NLPRGI) --- > REAL ADATA(NLPRGI),COLRNG(2,MCOLS) or through polarrfn.f-r1.45-r1.46.diff.
  • Bug fixes in Detwin
    Date : 14/11/2006
    CCP4 Version : 6.0.1
    System : all
    Level : minor
    Status : fixed
    Bugzilla number : #1775

    Some fixes for small bugs in Detwin have been provided by Pete Dunten. These include stopping Detwin from trying to detwin data when it does not have all of the reflection data required for detwinning and also a fix to prevent the java applet from breaking when no title is assigned and no twin fraction is assigned.

    The updated source code can be found here: detwin.f.

    (Thanks to Pete Dunten for reporting this problem and providing the updates to the source code.)

  • These are the known problems with release 4.2 of the CCP4 suite, together with fixes where appropriate. Code changes are given as patches, which can be applied with the UNIX patch utility. New files are put in the prerelease directory, which can be found at .

    Hints and advice about applying the fixes can be found here.

    If you can't find your problem here, please email us.

    Problems with current releases

    General and system specific problems

    A list of more general version-unspecific problems can be found The General Problems Page lists general version-unspecific problems as well as descriptions of various operating system-specific eccentricities.

    Warning for Linux users: if you are running CCP4 compiled with gcc 2.96 may be unreliable.. This has been seen with RedHat 7.0 and Mandrake 8.1.

    Problems with CCP4i

    A list of general and version-independent problems with CCP4i can be found here:

    Problems with MOSFLM

    As of CCP4 4.1, MOSFLM is being released as part of the CCP4 program suite; for problems on MOSFLM please refer to Harry Powell's MOSFLM page:

    Older versions of CCP4

    Older versions of the suite are not supported. The first step in attempting to solve a problem in older versions should be to upgrade to the current release. However, problems and fixes for older versions can be found here: Note that these pages are also unsupported and will most probably be out of date - particularly references to prerelease files.

    Other sources of information

    • Clemens Vonrhein's webpages have useful patches for some platforms not officially supported by the current release.


    Problems with 4.2.2


    Installation


    1. Mosflm shared build empty libjpeg.a
    Date : 24/02/2004
    CCP4 Version : 4.2
    System : all, during shared build
    Level : annoying
    Status : work around provided

    When ccp4 is build using --with-shared-lib the mosflm build can fail with

    Archive: ../jpg/libjpeg.a has no table of contents (not searched) this is due to the forced libjpeg.a make in the Mosflm makefile. A work around, after failed build, is as follows: cd $CCP4/x-windows/Mosflm/jpg make cp .libs/libjpeg.a . ranlib libjpeg.a cd .. make cd $CCP4 make install

    Programs


    1. Molrep sigsev
    Date : 27/11/2002,08/08/2003
    CCP4 Version : molrep 7.3, ccp4 4.2
    System : all, sigsev noted on OSF v5.0
    Level : serious
    Status : fix provided

    A typo in molrep.f leads to a scalar variable masquerading as an array. This may lead to the program failing with a sigsev error (though other failures have also been reported, for example: on Mac-OSX an 'Abort trap' may occur whilst reading sequential formatted internal IO).
    The fix is to apply the following patch and recompile molrep.

    diff -c -3 -r1.12.2.1 molrep.f *** molrep.f 2002/10/07 14:17:53 1.12.2.1 --- molrep.f 2002/11/27 11:29:53 *************** *** 9303,9309 **** ENDDO ENDIF ! CALL GET_CR_MATRIX(FRTOCR,CRTOFRF) IF(PROG.EQ.'CROS'.OR.PROG.EQ.'CRSL') THEN --- 9303,9309 ---- ENDDO ENDIF ! CALL GET_CR_MATRIX(FRTOCR,CRTOFR) IF(PROG.EQ.'CROS'.OR.PROG.EQ.'CRSL') THEN (Thanks to Phil Evans)
    2. Scala failure
    Date : 15/01/2003
    CCP4 Version : scala 3.1.20 and earlier, ccp4 4.2.2 and earlier
    System : all
    Level : only OUTPUT UNMERGED or SEPARATE
    Status : fix provided change to scala.f 17663c17663 < $ nrfrej, irogue, nstrej(13), nrunp1, ibtanl, ip, irn, nmpr, --- > $ nrfrej, irogue, nstrej(25), nrunp1, ibtanl, ip, irn, nmpr, 18172c18172 < do 18, i = 1,13 --- > do 18, i = 1,25 (Thanks to Phil Evans and Frank Vondelft)
    3. Refmac5 ``freezes'' at high resolution
    Date : 12/02/2003

    When Refmac 5.1.24 (or earlier) is run with a high resolution cutoff > 1.0A, a bug in the program forces it into an infinite loop - it appears to be running, but produces no output after reading in the libraries and will never finish.

    The workaround is to avoid using a high resolution cutoff above 1.0A. This bug will be fixed in future releases of Refmac5.

    (Thanks to Sue Roberts and Garib Murshudov)
    4. Molrep: LABIN PHIC=... fails
    Date : 18/03/2003

    The Molrep documentation states that you must use the PHIC label to specify phases, however this is incorrect - the program actually expects PHIB.

    (Thanks to Stephen Soisson)
    5. Watertidy: stalls when reading distang log file
    Date : 23/03/2003
    Version : CCP4 v4.2.2 and earlier
    System : all when run from command line
    Status : see parser problem

    (Thanks to Pete Dunten)


    6. Scala: use of FINAL SCAL has no effect
    Date : 02/06/2003
    Version : CCP4 v4.2.2
    System : all
    Status : fix provided
    Fix/Workaround : apply the following patch to $CCP4/src/scala_/scala.f diff -c -r1.63 scala.f *** scala.f 25 Jun 2002 16:24:11 -0000 1.63 --- scala.f 2 Jun 2003 07:53:40 -0000 *************** *** 10214,10219 **** --- 10214,10220 ---- if (lflag .eq. 0) then c A number read n = n+1 + lcorrc = .true. endif elseif (cvalue(n) .eq. 'CHEC') then kprflo = -min(iabs(kprflo), 10) *************** *** 10624,10629 **** --- 10625,10631 ---- c USE_PROFILE use profile-fitted intensity even for scaled partials c 410 n = 2 + lfinal = .true. lcorrc = .false. lprtst = .false. c lprscl is flag that SCALE_PARTIAL has been set *************** *** 10683,10688 **** --- 10685,10691 ---- prthou = prthld n = n+1 endif + lcorrc = .true. elseif (cvalue(n) .eq. 'USE_') then c Use profile-fitted intensities for scaled partials (only if present) if (ncip .gt. 0 .and. ncsdip .gt. 0) then
    7. Pdbset: reporting of coordinate limits
    Date : 08/08/2003
    Version : CCP4 v4.2.2
    System : all
    Status : fixed for 5.0
    Fix/Workaround PDBSET erroneously reports coordinates limits for input file, rather than for output file. This has been fixed and will be in 5.0. Meanwhile, the simplest solution is to re-run pdbset on the output file, with no keywords.
    8. Truncate fails using data harvesting
    Date : 15/08/2003
    Version : CCP4 v4.2.2
    System : IRIX with 64-bit compilation
    Status : not fixed

    Description TRUNCATE may fail when running with data harvesting turned on, for example with the error message .

    Fix/Workaround Currently there is no fix for this problem. The program will run if data harvesting is turned off.>


    CCP4i


    1. CCP4i can't find HOME on Windows
    Date : 28/11/2002

    CCP4i may fail to start on some Windows configurations, complaining that the HOME environment variable is not set or that it doesn't point to a valid directory. In fact, CCP4i doesn't need the HOME variable so this check is unnecessary.

    The fix is to download updated versions of and file from the prerelease area, where they can be found as ccp4i.tcl-4.2.2 and system.tcl-4.2.2.

    (Thanks to Jennifer Durkee for bringing this to our attention.)
    2. Merge Datasets/Merge MTZ Files Task (CAD)
    Date : 08/01/2003

    The option to reset HKL limits in the output MTZ file (in the ``Define MTZ Output folder) is incorrectly implemented. The correct implementation is for eitherthe Laue code or explicit HKL limits to be defined.

    The fix is to download updated versions of , and files from the prerelease area, where they can be found as cad.tcl-outlim, cad.def-outlim and cad.com-outlim.

    (Thanks to Eleanor Dodson for identifying the problem.)
    3. TCL8.4 catch with quotes
    Date : 03/01/2003

    CCP4i may have difficulty opening a task window, giving a stack trace

    can't read array(_element): no such element in array while executing "catch "set type $array($_element)" ... This is due to a difference in the effect of quotes versus braces between tcl8.4 and 8.3. The solution is to replace catch "..." with catch {...}. For the failure listed above the following changes should be made to ccp4i/src/utils.tcl *** utils.tcl 2002/04/04 14:35:59 1.11 --- utils.tcl 2003/01/21 13:26:35 1.12 *************** *** 293,301 **** set typelist {} if { [llength [set l [split $element ,] ] ] > 1 } { ! set status [catch "set type $array(_[lindex $l 0],0)"] } else { ! set status [catch "set type $array(_$element)"] } if { !$status && $type != "" && [info exists typedef($type)] } { --- 293,301 ---- set typelist {} if { [llength [set l [split $element ,] ] ] > 1 } { ! set status [catch {set type $array(_[lindex $l 0],0)}] } else { ! set status [catch {set type $array(_$element)}] } if { !$status && $type != "" && [info exists typedef($type)] } {
    4. Sigma-A Task Interface
    Date : 03/02/2003

    The specification of output MTZ labels are reversed for the two options of combining experimental and partial models and combining MIR data.

    The following changes should be made to $CCP4/ccp4i/tasks/sigmaa.tcl:

    *** sigmaa.tcl 2001/02/28 10:02:37 1.4 --- sigmaa.tcl 2003/02/03 09:48:32 1.5 *************** *** 284,290 **** CloseSubFrame ! OpenSubFrame frame -toggle_display SIGMAA_ACTION open COMB_PART CreateLaboutLine line \ "Combined phase angle and weight" \ --- 284,290 ---- CloseSubFrame ! OpenSubFrame frame -toggle_display SIGMAA_ACTION open COMB_MIR CreateLaboutLine line \ "Combined phase angle and weight" \ *************** *** 306,312 **** CloseSubFrame CloseSubFrame ! OpenSubFrame frame -toggle_display SIGMAA_ACTION open COMB_MIR CreateLaboutLine line \ "Combined Phase and weight" \ --- 306,312 ---- CloseSubFrame CloseSubFrame ! OpenSubFrame frame -toggle_display SIGMAA_ACTION open COMB_PART CreateLaboutLine line \ "Combined Phase and weight" \ (Thanks to Hiroto Yamaguchi)
    5. Molrep self rotation function
    Date : 01/09/03

    In Molrep, the keyword for inputting self-rotation function is FILE_TSR, but ccp4i writes FILE_SRF instead. The simple fix follows by change _SRF to _TSR:

    69c69 < 1 _FILE_SRF $SROT_SOLUTIONS --- > 1 _FILE_TSR $SROT_SOLUTIONS (thanks to Jade)
    6. REFMAC5 interface SIGB comments are incorrect
    Date : 14/04/04

    The comments associated with the TEMPerature factor restraints are incorrect, if followed the behaviour will not be as expected

    diff -r1.22 refmac5.tcl 1437c1437 < message "Enter weight for bonded Bfactor restraint (SIGB1)" \ --- > message "Enter weight for main chain bonded Bfactor restraint (SIGB1)" \ 1439c1439 < message "Enter weight for non-bonded Bfactor restraint (SIGB2)" \ --- > message "Enter weight for main chain non-bonded Bfactor restraint (SIGB2)" \ 1441c1441 < message "Enter weight for planar Bfactor restraint (SIGB3)" \ --- > message "Enter weight for side chain bonded Bfactor restraint (SIGB3)" \ 1443c1443 < message "Enter weight for Bfactor restraint involving an hydrogen atom (SIGB4)" \ --- > message "Enter weight for side chain non-bonded Bfactor restraint (SIGB4)" \ Similarly the refmac5 documentation is incorrect; with the SIGB2 and SIGB3 definitions reversed.
    (thanks to George Phillips)

    Libraries


    1. parser.f: incorrect treatment of comments
    Date : 23/04/03
    Version : CCP4 v4.2.2 and earlier
    System : all
    Status : fix provided

    The parser incorrectly treated comment lines and lines containing a single token before a comment. This lead to attempts to read from stdin when a non-blank input line was sent to the parser routine.

    Apply the following patch to $CCP4/lib/src/parser.f

    *************** *** 294,300 **** NINCHR = 0 ENDIF FIRST = .TRUE. ! GO TO 20 END IF C C---- Test if first field begins '@' and include file if so --- 294,300 ---- NINCHR = 0 ENDIF FIRST = .TRUE. ! IF(LENLIN.EQ.0) GO TO 20 END IF C C---- Test if first field begins '@' and include file if so *************** *** 533,539 **** + (LINE(I:I).EQ.ICOMM1 .OR. LINE(I:I).EQ.ICOMM2)) THEN COMMNT = .TRUE. C special case; comment line: ! IF (N.EQ.1) THEN N = 0 RETURN END IF --- 533,539 ---- + (LINE(I:I).EQ.ICOMM1 .OR. LINE(I:I).EQ.ICOMM2)) THEN COMMNT = .TRUE. C special case; comment line: ! IF (I.EQ.1) THEN N = 0 RETURN END IF

    Documentation, Tutorials and Examples


    1. FFT Program Documentation
    Date : 07/01/2003

    The second reference given in the documentation has the incorrect page number. The reference should be:

  • L.F.Ten Eyck, Acta Cryst., A29, 183, (1973).
  • (Thanks to Herbert Bernstein for bringing this to our attention.)

    Problems with 4.2.1


    Installation


    1. Mosflm fails to compile under linux with shared libraries.
    Date : 25/06/2002 Version CCP4 versions 4.2.0 and 4.2.1

    Mosflm fails to link correctly against libccp4.so on linux. The resulting errors are of the form

    /xtal/ccp4-4.2/lib/src/libccp4.so: undefined reference to `ccif_new_cif_' This would seem to be due to the linker loading the whole library, not just those modules necessary. The solution is to add -L<libccif location> -lccif to the MOSLIBS entry of mosflm/Makefile. A partial fix is in version 4.2.1. The latest Mosflm/configure and Mosflm/mosflm/Makefile.in are available mosflm_link.tar.gz. (Thanks to Todd Geders for informing us of the problem)
    2. LAPACK/BLAS configuration
    Date : 30/07/2002

    There is a potential problem with the LAPACK configuration when upgrading from 4.2 to 4.2.1.

    If the original installation created LAPACK and/or BLAS libraries from the Netlib source code then it may be that configure detects these when upgrading, but fails to write the information to the Makefile headers - resulting in compilation errors for e.g. SCALA complaining that slamch or ssyev are unresolvable symbols.

    The fix is to download the updated file from the prerelease area.

    (Thanks to Sandra McLaughlin for informing us of the problem)

    Programs


    1. Scala.
    Date : 12/07/2002
    Version : CCP4 4.2 and 4.2.1, SCALA pre 3.1.11

    When processing a mtz file containing batches belonging to a single dataset with dataset number is 0 scala may experience runtime sigsev or bus errors. Behaviour on other systems is undefined.
    The fix is to apply the following patch to :

    diff -c -r1.63 scala.f *** scala.f 2002/06/25 16:24:11 1.63 --- scala.f 2002/07/12 08:41:35 *************** *** 22167,22174 **** $ ' for batch ', ibatch call ccperr(1,'*** Invalid batch dataset number ***') else ! c Dataset ID unset ! j = 0 endif c 5 jdtsbt(i) = j --- 22167,22183 ---- $ ' for batch ', ibatch call ccperr(1,'*** Invalid batch dataset number ***') else ! c Dataset ID unset, set it to 1 (ie everything is one dataset) ! if (ndatasets .gt. 1) then ! c Can't do this if there is more than one dataset ! write (6, '(/a,a/)') ! $ ' ERROR: the file contains multiple datasets', ! $ ' but batches are not assigned to datasets (SETCRY)' ! call ccperr ! $ (1, '*** batches not assigned to datasets ***') ! endif ! j = 1 ! idtsbt(i) = j endif c 5 jdtsbt(i) = j This problem is also fixed in from the prerelease area as .
    (Thanks to Phil Evans.)
    2. professs
    Date : 31/07/2002

    TIDY keyword broken.

    The problem appears as below: Data line--- tidy orth 30 20 10 *** Warning No argument expected Data line--- END professs: Input error (see above) professs: Input error (see above) Times: User: 0.1s System: 0.1s Elapsed: 0:00 Solution - make the following change: 101c101 < call parsekey('TIDY',tidyin) --- > call parsesubkey('TIDY',' ',tidyin) (Thanks to Pete Dunten for pointing this out)
    3. cif2mtz
    Date : 08/08/2002

    LABOUT keyword broken.

    You can omit the LABOUT keyword and change the labels later with CAD, or there is an updated program on the prerelease area.


    4. combat.
    Date : 27/08/2002

    COMBAT doesn't process XDET, YDET and ROT values correctly. This was originally reported for input from SAINT but is probably a bug for all input formats.

    The fix is the following patch to be applied to :

    *** combat.f 2002/06/14 14:31:30 1.14 --- combat.f 2002/08/27 10:04:21 *************** *** 939,951 **** xdetmn = min(xdetmn, xdet) ydetmn = min(ydetmn, ydet) phimax = max(phimax, fphi) - else - C set ROT equal to batch. - adata(13) = adata(5) phimin = min(phimin, fphi) adata(11) = xdet adata(12) = ydet adata(13) = fphi endif c write out reflection for monitoring --- 939,951 ---- xdetmn = min(xdetmn, xdet) ydetmn = min(ydetmn, ydet) phimax = max(phimax, fphi) phimin = min(phimin, fphi) adata(11) = xdet adata(12) = ydet adata(13) = fphi + else + C set ROT equal to batch. + adata(13) = adata(5) endif c write out reflection for monitoring (Many thanks to Toshihiko Akiba)
    5. sftools
    Date : 12/09/2002

    There is a minor bug when converting CNS Rfree to MTZ, if the file contains reflections with zero sigma. The program prints a warning and then fails to perform the conversion.

    The bug is fixed by installing the updated file from the prerelease area.

    (Thanks to Ezra Peisach and Bart Hazes)
    6. ipdisp script
    Date : 20/09/2002
    Version : CCP4 v4.2.1 and earlier
    System : Tru64 Bourne shell, possibly Bourne shell general
    Status : fix provided

    The ipdisp scritp has been found to fail with the detault Bourne shell on Tru64. This is due to a problem with the expansion of "$@". The solution is to replace "$@" with ${1+"$@"} for all occurences.

    (thanks to Dave Love for finding the problem and providing the fix)


    7. sigmaa PARTIAL DAMP weights not applied when DAMP is lower case
    Date : 27/09/2002
    Version : CCP4 v4.2.1 and earlier
    System : all
    Status : work around and fix provided. Fixed in subsequent release.

    When using damping with PARTIAL, the damp keywork is not recognised if it is in lower case.

    Workaround: use upper case.

    Fix: apply the following patch to $CCP4/src/sigmaa.f.

    diff -c -r1.51 -r1.50 *** sigmaa.f 2002/09/27 09:50:21 1.51 --- sigmaa.f 2002/08/08 13:20:22 1.50 *************** *** 556,563 **** ICOMB = 0 ICHANG = 0 C DAMP D1 ( D2 ( D3) ) (Thanks to Yamaguchi Hiroto for providing the fix)
    8. Peakmax
    Date : 02/10/2002

    The OUTPUT PDB option of PEAKMAX doesn't align the atom name in the correct column of the output file. This causes unecessary warnings in other programs, for example WATPEAK, which use the file as input.

    The following patch applied to fixes the problem:

    diff -u -r1.41 peakmax.f --- peakmax.f 2002/08/06 12:20:24 1.41 +++ peakmax.f 2002/10/02 14:34:01 @@ -216,7 +216,7 @@ + NYc,NZEROPK,NZ1,NZ2,NZC,SX1,SX2,SY1,SY2,LFLAG,IST LOGICAL LEND,LIMS,LRMS, LBFAC, LFIRST, LFRAC, LPEAK, XMLOUT CHARACTER IDCH*1,ID*4,ATNAM*4,KEY*4,RESTYP*4,LINE*400,RESNO*4, - + ALTCOD*1,SEGID*4,INSCOD*1 + + ALTCOD*1,SEGID*4,INSCOD*1,ATMTYP*4 C .. C .. Local Arrays .. INTEGER MAXPK @@ -309,6 +309,7 @@ LFRAC = .FALSE. LPEAK = .FALSE. ATNAM = ' O' + ATMTYP = ' O ' RESTYP = 'HOH' IDCH = 'X' BS(1) = 30.0 @@ -922,7 +923,7 @@ END IF END IF CALL XYZATOM(IXYZOUT,ISER,ATNAM,RESTYP,IDCH,IRES,RESNO, - $ INSCOD,ALTCOD,SEGID,IZ,ID) + $ INSCOD,ALTCOD,SEGID,IZ,ATMTYP) CALL XYZCOORD(IXYZOUT,'O','U',XX,YY,ZZ,QOCC,BISO,BS) CALL XYZADVANCE(IXYZOUT,0,0,*310,*310) IRES = IRES + 1 (Thanks to Phil Evans)
    9. molrep, RAD keyword does not work
    Date : 07/10/2002
    Version : CCP4 v4.2.1, molrep version 7.3.0-02
    System : all
    Status : Fixed in molrep 7.3.03, fix provided.

    The keyword RAD has no effect, it is overridden by the default value. The fix follows, in $CCP4/src/molrep_/main_molrep_mtz.f:

    1988c1988 < RAD = FVALUE(2) --- > ARAD = FVALUE(2) (Thanks to Yamaguchi Hiroto)
    10. contact, missing contacts
    Date : 06/11/2002
    Version : CCP4 v4.2.1 and earlier
    System : all
    Status : Under investigation, work around provided.

    Contact will fail to identify contacts to main chain atoms in different chains if the residue number differs by less than 2.

    The work around is to renumber the residues so that the numbers do not overlap. (Thanks to Mats Okvist



    CCP4i


    1. FFT/FFTBIG interface
    Date : 18/07/2002

    When CCP4i generates a keyworded script for FFT which excludes structure amplitudes below a certain minimum, it writes EXCLUDE F1MIN. In fact the correct keyword is EXCLUDE F1LIM.

    Apply the following patch to :

    diff -r1.5 -r1.5.2.1 27,28c27,28 < -- {[IfSet $EXCLUDE_MINIMUM_1]} f1min $EXCLUDE_MINIMUM_1 < -- {[IfSet $EXCLUDE_MINIMUM_2]} f2min $EXCLUDE_MINIMUM_2 --- > -- {[IfSet $EXCLUDE_MINIMUM_1]} f1lim $EXCLUDE_MINIMUM_1 > -- {[IfSet $EXCLUDE_MINIMUM_2]} f2lim $EXCLUDE_MINIMUM_2 (Thanks to Eleanor Dodson)
    2. Corrupted database/database.LOCK
    Date : 19/07/02

    There are two minor bugs:

    1. CCP4i only checks that the database.def file for the current project is "valid" on startup, not when changing between projects in a session.
    2. In some circumstances the database.LOCK file for a project may be deleted inappropriately, preventing warnings when multiple CCP4i processes try to access the same project database.

    The problems are fixed by updated versions of and , available from the prerelease area as and .


    3. Prepate Data for HA: incorrect column labels for "SAD data as Dano" option.
    Data : 02/09/02
    Version : CCP4 v4.2 and 4.2.1

    For the Prepare Data for HA task the wrong column labels are returned for SAD data as Dano outputing SHELX format. The correction is to apply the following patch to $CCP4/ccp4i/scripts/prephadata.script

    diff -c -r1.5 prephadata.script *** prephadata.script 2002/04/03 09:07:14 1.5 --- prephadata.script 2002/09/02 12:34:06 *************** *** 106,112 **** set FP FM set SIGFP SIGFM } elseif { [StringSame $REVISE_INPUT SADDS] } { ! set LABIN "FPH SIGFPH FP SIGFP" } elseif { [StringSame $REVISE_INPUT SIR] } { set LABIN "FPH SIGFPH FP SIGFP" } elseif { [StringSame $REVISE_INPUT NATIVE] } { --- 106,116 ---- set FP FM set SIGFP SIGFM } elseif { [StringSame $REVISE_INPUT SADDS] } { ! set LABIN "DP SIGDP" ! unset DP ! unset SIGDP ! set DP $ECALC_DPH0 ! set SIGDP $ECALC_SIGDPH0 } elseif { [StringSame $REVISE_INPUT SIR] } { set LABIN "FPH SIGFPH FP SIGFP" } elseif { [StringSame $REVISE_INPUT NATIVE] } {
    4. Sigma-A: combining isomorphous phases with structure factors generated by SFALL
    Data : 02/09/02
    Version : CCP4 v4.1.x, 4.2 and 4.2.1

    Attempts to use SFALL generated structure factors with the "combine isomorphous phase with partial solution" or "combine two sets of MIR phases" fail as there are missing labels at the SIGMAA stage. This is because only the F SIGF RFREE FC and PHIC labels are included in the temporary mtz file.
    The solutions are:

    • Run SFALL and SIGMAA seperately, including all columns in the SFALL gernated mtz file, or
    • Apply the following patch to $CCP4/ccp4i/scripts/sigmaa.script diff -r1.2 sigmaa.script 15a16,20 > > if { $SIGMAA_ACTION != "PART" } { > set ALLIN 1 > } >

    5. Monomer Library Sketcher
    Date : 10/09/2002

    Two problems:

    1. If the sketched monomer contains aromatic bonds (possibly other "unusual" types e.g. "delocalised" or "metal") then "Create Dictionary Entry" will fail to create the output dictionary file.
    2. In some cases the atom type in the Sketcher is mixed case (e.g. Cl for chlorine), however the program expects uppercase names so the atom type is incorrectly transfered to the output file.

    Both problems are addressed by applying the following patch to $CCP4/ccp4i/sketch/dictionary.tcl:

    --- dictionary.tcl 2002/05/21 07:42:30 1.6 +++ dictionary.tcl 2002/09/10 14:37:40 1.6.2.2 @@ -426,7 +426,7 @@ for { set n 1 } { $n <= $Mol(nAtoms) } { incr n } { append text " $Mol(chem_comp_id) [write_cif_name $Mol(Name,$n)]" foreach output $output_list { - append text " " $Mol($output,$n) + append text " " [string toupper $Mol($output,$n)] } append text \n } @@ -441,7 +441,7 @@ for { set n 1 } { $n <= $Mol(nBonds)} { incr n } { set a1 [lindex $Mol(Bonds,$n) 0] set a2 [lindex $Mol(Bonds,$n) 1] - set type [lindex [list nowt single double triple] $Mol(Bondtype,$n)] + set type [lindex [list nowt single double triple delocalised aromatic metal coval] $Mol(Bondtype,$n)] append text " $Mol(chem_comp_id) [write_cif_name $Mol(Name,$a1)] [write_cif_name $Mol(Name,$a2)] $type\n" } (Thanks to Liz Potterton)
    6. Missing files in ``View Files from Job'' when running e.g. ARP/wARP
    Date : 17/09/2002

    There is an occassional problem when starting a job within CCP4i and then closing down the main interface while it runs - upon restarting the interface and going to the ``View Files from Job'' menu, some of the output files may not be listed.

    This is particularly a problem for interfaces such as ARP/wARP, which rely heavily on registering output files with CCP4i whilst the task is running, however it could potentially occur with other tasks too. The log file for the job may also contain messages of the form:

    ERROR running script can not connect to server port SERVER_HOST localhost SERVER_PORT 4441

    A workaround is not to close the main CCP4i window until the job has finished running. A more useful fix can be effected by downloading updated versions of the files , , and (all should be put into the directory). The files can be found on the prerelease area as database-buffer.tcl, execute-buffer.tcl, task-buffer.tcl and taskbrowser-buffer.tcl.


    7. Failure with mulitple domains for dmmulti interface
    Date : 27/09/2002
    Version : CCP4I version 1.3.8 (CCP4 v4.2.1) and previous to 1.2.6 System : all Status : fixed in subsequent releases, fix provided

    The ccp4i dmmulti interface will fail to run multiple domain jobs with the error message:

    Error:can't read "array(MASKIN,1MASKIN,2)": no such element in array

    The fix is to apply the following to $CCP4/ccp4i/tasks/dmmulti.tcl:

    76c76 < append array(INPUT_FILES) "MASKIN,$n" --- > append array(INPUT_FILES) "MASKIN,$n " (Thanks to Yamaguchi Hiroto for the fix)
    8. Molrep
    Date : 30/09/2002

    When inputing fixed monomers in the Molrep interface, the option fails (although the program runs to completion) and the log file contains the warning

    The error is because the file with the fixed monomers should be supplied on the command line rather than via a keyword. The following patches will fix the problem:

    To $CCP4/ccp4i/scripts/molrep.script:

    diff -u -r1.5 molrep.script --- molrep.script 2002/04/23 09:32:36 1.5 +++ molrep.script 2002/09/30 13:48:29 @@ -59,6 +59,9 @@ if { [StringSame $MOLREP_MODE FIT] } { append cmd " MODEL2 $XYZIN2" } + if { [StringSame $IFFIXED 1] } { + append cmd " MODEL2 $XYZFIXED" + } CreateComScript molrep molrep_script set status [Execute $cmd $molrep_script program_status report]

    To $CCP4/ccp4i/templates/molrep.com:

    diff -u -r1.8 molrep.com --- molrep.com 2002/04/23 09:32:39 1.8 +++ molrep.com 2002/09/30 13:49:14 @@ -17,9 +17,6 @@ ENDIF ENDIF -$IFFIXED _MODEL_2 $XYZFIXED -{[IfSet $FUNCTION] && ![StringSame $FUNCTION A]} FUN $FUNCTION - IF { ![StringSame N $PSEUDO_TRANS_MODE] } 1 PST $PSEUDO_TRANS_MODE {[IfSet $PSEUDO_TRANS] } VPST $PSEUDO_TRANS (Thanks to Akihiro Okamoto for finding and fixing the problem.)
    9. Errors/anomalous behaviour when closing task windows
    Date : 16/10/2002

    In certain circumstances Tcl errors of the form:

    array(WINDOW) not found may appear when closing task windows. In other circumstances closing one window may cause a second window to close simultaneously. These problems have been observed when a task window has been invoked from the task list and at the same time another window has been opened to rerun the same task.

    Both problems can be fixed by installing an updated file in . The file can be found on the prerelease area as .

    NB. this updated file includes the fix from the previously reported problem regarding Corrupted database/database.LOCK.


    10. Rerunning BEAST job
    Date : 21/10/2002

    Under certain circumstances there may be problems with recovering the correct parameters when rerunning an earlier BEAST job, for example: if the original job involved running a rotation search on molecule then the rerun parameters will change this to .

    The problem is fixed by installing an updated file in . The file can be found on the prerelease area as .

    (Thanks to Randy Read for reporting the problem.)

    Libraries


    1. Uninitialized IERR in LRASSN
    Date : 26/09/2002
    Version : CCP4 version 4.2.1
    System : so far Suse 7.3 using gcc2.95.3, but possibly others
    Status : fixed in subsequent releases, fix provided

    An uninitialized variable in LRASSN may cause program exit

    Error in label assignments when no user LABIN line is required (SCALA, COMBAT).

    The fix is to apply the following to mtzlib.f:

    *************** *** 545,550 **** --- 545,551 ---- C---- First loop over user input labels and assign them to file labels C If NLUSRI(MINDX)=0 then this loop is never executed C + IERR = 0 DO 70 JDO50 = 1,NLPRGI CWORK = LSUSRI(MINDX,JDO50) IF ((NLUSRI(MINDX).GT.0) .AND. (CWORK.NE.' ')) THEN

    Documentation, Tutorials and Examples


    1. $CEXAM/tutorial2000/data/gere_nat.mtz
    Date : 13/11/02

    This file is supposed to be used as example input to the program TRUNCATE. However, the file contains unmerged data (with batch information) and is not appropriate. In fact, the tutorial can be run with this file, but don't look too closely at the output!




    Problems with 4.2


    Installation


    1. Shared vs static libraries on IRIX 6.5 n32.
    Date : 01/05/2002

    If you are running on IRIX 6.5 then you will always get a shared version of even if shared libs were not requested via the option.

    The fix is to apply the following patch to :

    diff -r1.165 configure 630,631c630,634 < SHARED_LIB_FLAGS=${SHARED_LIB_FLAGS-'-n32 -mips3'} < SHARE_LIB=${SHARE_LIB-'ld -n32 -mips3 -shared -all libccp4.a -o libccp4.so'} --- > # Shared libraries only if requested > if test "$shared_lib" = yes; then > SHARED_LIB_FLAGS=${SHARED_LIB_FLAGS-'-n32 -mips3'} > SHARE_LIB=${SHARE_LIB-'ld -n32 -mips3 -shared -all libccp4.a -o libccp4.so'} > fi and then rebuild by running , then make etc.

    NB. you will need to delete the and files before rebuilding.


    2. TMPDIR not defined on IRIX.
    Date : 07/05/2002

    We have had several reports of compilation failing on IRIX with Error Code 127 (bu21), or Error Code 2 (bu21). Sometimes this will be accompanied with TMPDIR undefined. The solution is to set TMPDIR during the configuration, eg

    configure irix64 --with-x --tmpdir=/tmp/XXX (Thanks to Jonathon Dill)
    3. Mosflm fails to compile for -64 IRIX.
    Date : 24/05/2002

    Several FFLAGS and CFLAGS are missing from the x-windows/Mosflm/mosflm Makefile.in . This results in mosflm failing to compile for irix64 due to several of the produced objects being -n32. Replace x-windows/Mosflm/mosflm/Makefile.in with the version on the prerelease area.

    If make has already been run; delete the *.o files in x-windows/Mosflm/mosflm, then execute config.status in x-windows/Mosflm, followed by make in x-windows/Mosflm/mosflm .


    4. MapSlicer configure doesn't find Tk library
    Date : 17/06/2002

    When the main CCP4 configure tries to set up to build the MapSlicer Tcl command library, it may fail to find an appropriate Tk library even though one exists on the system.

    This is due to a bug in the , and can be addressed by applying the following patch:

    diff -r1.171 configure 2215,2216c2215,2216 < # ... and possible versions for tk < for testvers in $tryvers --- > # ... and possible extensions for tk > for testext in $tryexts (Thanks to Michael Strickler)

    Programs


    1. Scala.
    Date : 07/05/2002

    There is a buffer size problem which manifests itself as a fatal error on attempting to write a scratch file, if there are 5 or more datasets. The fix is to :

    diff ../scala_4.2/dts_storage.fh . 20c20 < common /dts_storage/ dts_data(maxsets*4+4), --- > common /dts_storage/ dts_data(maxsets*5+4), (Thanks to Phil Evans.)
    2. MOSFLM
    Date : 16/05/2002

    Mosflm no longer handles R3 or R32 (hexagonal setting) properly because of the changes in the symop.lib file in CCP4 4.2. (H3 and H32 aren't handled in any release version of Mosflm.)

    Anyone who has an MTZ file for R3 or R32 created more than a couple of weeks ago will find that the symmetry is broken, and they have to use MTZUTILS or CAD to change the space group as appropriate.

    (Harry Powell)
    3. AstexViewer
    Date : 28/06/2002

    Although the documentation suggests that it possible to run AstexViewer as a standalone application, there are problems doing this - you get an error of the form

    Exception in thread "main" java.lang.NoClassDefFoundError: MoleculeViewer

    The problem is fixed by picking up a new version of the AstexViewer.jar file from the prerelease area. This replaces the version in (and , if you have already performed the installation).

    (Thanks to Mike Hartshorn)
    4. procheck/anglen, procheck/bplot
    Date : 28/06/02
    Version : CCP4 v4.2, fixed in v4.2.1

    anglen fails with a segv or gives incorrect results. This is corrected using the following patch which reinstates the presistance of data for calls of STORAT and STORPL.

    diff -c -2 -r1.9 anglen.f *** anglen.f 2002/02/25 10:04:32 1.9 --- anglen.f 2002/06/28 13:43:51 *************** *** 742,745 **** --- 742,747 ---- SUBROUTINE STORAT(IRESID,RSNAME,INCHN,INSEQ,IBAT,COORDS,NEWCHN) + SAVE CHAIN, FILLED, XYZ, RNAME, SEQNO, SRESID + INCLUDE 'anglen.inc' *************** *** 1076,1079 **** --- 1078,1083 ---- SUBROUTINE STORPL(IRESID,RSNAME,ATNAM,INCHN,INSEQ,COORDS,NEWCHN) + SAVE CHAIN, NGOT, FILLED, XYZ, SEQNO, SNAME, SRESID, PLRES + INCLUDE 'anglen.inc' Also for bplot.f, subroutine REAPLN diff -c -2 -r1.5 -r1.6 *** bplot.f 2002/02/25 10:04:32 1.5 --- bplot.f 2002/07/02 08:42:43 1.6 ********************** *** 2638,2641 **** --- 2641,2646 ---- SUBROUTINE REAPLN(LINE,RMS,LMAIN,LSTCHN,LSTRES,LSTSEQ,FOUND, - COORD,ANAME,NATOM,ENDFIL) + + SAVE IREC, IATOM INCLUDE 'bplot.inc' (Thanks to Fukami Takaaki)
    5. REFMAC
    Date : 16/07/2002

    There are a few cases of Refmac 5.1.19 (distributed with CCP4 4.2) terminating with the error:

    Too many atoms in one brick. Maximum allowed in one brick = 60 Check symmetry, cell dimensions ===> Error: CREATE_NET failed I'm not sure what the cause of this problem is, but it appears to have been cured in Refmac 5.1.24 (distributed with CCP4 4.2.1). The advice is therefore to upgrade!

    However be aware that the message may be genuine. One user reports inserting sequence with mut_ins in , but not building them. Thus, there were greater than 60 atoms at 0, 0, 0 and refmac5 correctly complained!

    (Martyn Winn)


    CCP4i


    1. Mapcutting Task.
    Date : 01/05/2002

    The mapcutting task fails due to a broken .def file, apply the following patch to :

    *** mapcutting.def 2002/03/07 10:03:12 1.1 --- mapcutting.def 2002/05/01 15:02:33 *************** *** 43,48 **** --- 43,49 ---- NCS_OP_XTRAN,0 _real "" NCS_OP_YTRAN,0 _real "" NCS_OP_ZTRAN,0 _real "" + NCS_OP_CONVENTION,1 _text POLAR NCS_OP_ALPHA,1 _real 0.0 NCS_OP_BETA,1 _real 0.0 NCS_OP_GAMMA,1 _real 0.0 (Thanks to Kevin Cowtan)
    2. Monomer Library Sketcher.
    Date : 13/05/2002

    There are two reported problems:

    1. Using Tk version < 8.3 there is an error message Error: unknown option "-dash" when stepping through bond types by clicking on the bond.
      Download the fixed file from the prerelease area.
    2. The delocalised & aromatic bond types don't get written to the bondlist.cif file when you click on "Create library description".
      Download the fixed file from the prerelease area.
    (Liz Potterton)
    3. Convert to MTZ & Standardise Task.
    Date : 08/05/2002

    The task fails with ERROR no type for ANOMALOUS. This is corrected by appling the following patch to :

    *** import.def 2002/01/30 15:17:41 1.5 --- import.def 2002/05/08 10:54:59 *************** *** 70,75 **** --- 70,76 ---- FALLOFF _logical 1 RUN_UNIQUE _logical 1 + ANOMALOUS _logical 1 UNIQUE_INPUT _MTZ_file "" UNIQUE_OUT _MTZ_file "" FREER_MODE _freer_mode 2
    4. Generate Patterson Map Task (possibly more general).
    Date : 16/05/2002

    If the "Plot default Harker map sections with coordinates of peaks in map" option is chosen for orthorhombic spacegroups, then the task fails with an error message from MSYMLB3. This is basically because the Patterson spacegroup occupies more space in the CRYST1 line of the PDB file than is allowed for. There is a fix to the library file to deal with this case.

    Download the fixed file from the prerelease area, and re-compile the CCP4 library. If you have compiled statically, then you will need to re-compile at least the executable against the fixed library.


    5. lsqkab graphs.
    Date : 16/05/2002

    When running lsqkab through ccp4i (superpose) the requested rms table will not display under loggraph. This is due to a double processing of the output table, which results in two headers. A quick fix is to remove the second header. A version of superpose.script which fixes this problem is on the prerelease area.


    6. dm
    Date : 16/05/2002

    When running with NCS averaging and the option to Create file to display NCS operators in [...] format, the options are reversed i.e. requesting "XtalView" results in an "O" macro and vice versa.

    The following patch applied to fixes the problem:

    diff -r1.7 dm.tcl 39c39 < set typedef(_dm_vuout_format) { menu { O XtalView } { vu odat } } --- > set typedef(_dm_vuout_format) { menu { O XtalView } { odat vu } } (Thanks to Kevin Cowtan)
    7. Refmac5
    Date : 20/05/2002

    When running in "review" mode, the interface may complain that no harvest information is set even though there is no where in the window to enter it.

    The following patch applied to will fix this behaviour:

    diff -r1.20 -r1.21 65,66c65,66 < # Check harvesting if not running idealisation (and harvesting is selected) < if { ![StringSame $refine_type IDEA] && \ --- > # Check harvesting if not running idealisation or review (and harvesting is selected) > if { ![StringSame $refine_type IDEA REVIEW] && \
    8. Tcl errors when using "ReRun" option
    Date : 20/06/2002

    This affects all versions of CCP4i - in certain circumstances (e.g. trying to open a task window using the "rerun job" option), you get a Tcl error dialogue window with a message of the form:

    can't set "array(REFINE_TYPE)": bad window path name ".w_dbtmp_2.main.canvas.contents.param_1" and the task window doesn't appear.

    This seems to happens when the task window has previously been closed using the window manager control (e.g. the "X" close button on the top right of the window frame on Linux systems) rather than the "Close" button at the bottom of the window.

    The errant behaviour is fixed by applying the following patch to :

    diff -r1.8 -r1.9 166d165 < 377a377,388 > # Bind destroy event to be consistent with the use of the > # Dismiss button above > # NB > # You can't just do "bind $w <Destroy> "..."" because all the > # children of $w also inherit the binding - so this construct > # (borrowed from Harrison and McLennan's "Effective Tcl/Tk > # Programming") defines a new bindtag and gives this to $w only > bind destroyTaskWindow <Destroy> \ > "UnsetArrayExtras $arrayname > DeleteTaskWindow $w $arrayname $taskname" > set tags [bindtags $w] > bindtags $w [linsert $tags 0 destroyTaskWindow] (or by avoiding use of the window manager close control).(Thanks to Kevin Cowtan)
    9. Scala/Scale Experimental Intensities task
    Date : 01/07/2002, 11/07/2002
    1. In some cases there is a problem with output MTZ files from MOSFLM being fed into SCALA.

      SCALA now uses information about datasets in the input MTZ file: if multiple datasets are present (from multiple runs of MOSFLM), the default is to scale tham together but split them into separate output files (this is intended for MAD datasets). In MOSFLM, if the user doesn't specify project and dataset names for runs, then the program gives each run a unique project and dataset name based on the date and time.

      The problem occurs when these runs are sorted together and put into SCALA. By default SCALA treats each dataset independently, and outputs two MTZ files with names based on the dataset names from the input file: this is confusing if you wanted to just scale all the data together.

      The ounce of prevention is to make sure that you explicitly set appropriate project and dataset names when running MOSFLM, using the PNAME & DNAME commands.

      The pound of cure (workaround) using the existing SCALA gui is to define separate runs (the default "run 1 all" is OK for this purpose) and assign this run to a single output project/dataset (ie delete all but one dataset & give it a sensible name). Alternatively REBATCH can be used to reset the project and dataset names before running (but be aware that this options are not currently available through the REBATCH gui and must be scripted manually). If you are running SCALA with a script, add a command line

      name project <project_name> dataset <dataset_name> to force all data into a single dataset.

      An updated version of the SCALA interface has a new option to combine all input datasets into a single output dataset, which should solve the problem - this can be obtained from the prerelease area and requires the files , ,

      (Thanks to Phil Evans)
    2. There is a problem if the input MTZ file contains a single dataset but multiple `runs' have been defined with several output datasets. In this case the interface generates additional unwanted PNAME/DNAME commands in the script which means Scala outputs a single dataset instead.

      A second problem is that when using "Rerun" for these jobs, the details of output datasets (and of which run is assigned to which dataset) seem to be lost or overwritten.

      Both these are fixed by an updated version of the SCALA interface file , which can be

    3. obtained from the prerelease area. This version also contains the fixes for the previous problems (see above).

    10. Kill Job fails on SunOS/Mac OS-X;CCP4i help pages don't work with Netscape under KDE (Linux)
    Date : 01/07/2002

    Two problems:

    1. Kill Job doesn't work on SunOS and Mac OS-X systems;
    2. Help pages fail to appear when running CCP4i on Linux under the KDE desktop.

    Both problems can be fixed by replacing the existing file with the version on the prerelease area.


    Libraries


    1. Parser.f
    Date : 06:06:2002

    The @filename instruction in the parser only uses the first 61 characters of the string. This means long filenames cannot be used. The solution is to increase the dimension of the CHARACTER array used to store the filename in parser.f.

    169c169 < CHARACTER FLNAME*60,LINEX*1500,LINEK1,SLASH --- > CHARACTER FLNAME*256,LINEX*1500,LINEK1,SLASH
    2. cciflib.f string handling error
    Date : 28:06:2002
    Version : CCP4 4.0 -> 4.2 . Fixed in 4.2.1

    In ccp4ccif_setup_context a passed fortran character string is given a fixed length. This is bad coding practice. As additional memory may be grabbed for the string, leading to undefined behaviour.

    This may have manifested itself in some cif2mtz problems, eg

    >>>> CCIF signal CCIF_NOITEM (severity: Warning) <<<< (Raised in ccif_setup_context) Data name or category "REFLNFound column with label and type Column " not defined in dictionary

    Apply the following correction to cciflib.f:

    diff -r1.6 cciflib.f 3153,3154c3153,3154 < character*(cfllen) catnam_in,catnam_out < character*(*) disposition --- > character*(cfllen) catnam_out > character*(*) disposition, catnam_in Users of the GNU compiler set will be required to make the following additional changes: 3166,3168c3166,3168 < write(ERRLINE,*) < + ' Warning in ccp4ccif_setup_context: Category '// < + catnam_in(1:lenstr(catnam_in))//' not present in data block.' --- > write(ERRLINE,"(A,A,A)") > + ' Warning in ccp4ccif_setup_context: Category ', > + catnam_in,' not present in data block.' 3175,3176c3175,3177 < write(ERRLINE,*) ' Error in ccp4ccif_setup_context: '// < + 'Tried to set up category '//catnam_in(1:lenstr(catnam_in))// --- > write(ERRLINE,"(A,A,A)") > + ' Error in ccp4ccif_setup_context: '// > + 'Tried to set up category ',catnam_in, 3184,3185c3185,3187 < write(ERRLINE,*) ' Error in ccp4ccif_setup_context: '// < + 'Tried to set up category '//catnam_in(1:lenstr(catnam_in))// --- > write(ERRLINE,"(A,A,A)") > + ' Error in ccp4ccif_setup_context: '// > + 'Tried to set up category ',catnam_in, 3191,3193c3193,3196 < write(ERRLINE,*) ' Error in ccp4ccif_setup_context: '// < + 'Unexpected context type for category '// < + catnam_in(1:lenstr(catnam_in)) --- > write(ERRLINE,"(A,A)") > + ' Error in ccp4ccif_setup_context: '// > + 'Unexpected context type for category ', > + catnam_in (Thanks to Avi Naim)

    Documentation, Tutorials and Examples


    1. Harvesting Implementation documentation
    Date : 16/05/2002

    The documentation for "Implementing Data Harvesting" is missing from the programmers documentation for CCP4i.

    The file can be fetched from the prerelease area.

    (Thanks to Maria Turkenburg)

    In addition there are some more technical known bugs which have not been dealt with at present but may not be noticable on your machine.

    CCP4 Main Page

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