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Collaborative Computational Project No. 4 |
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Collaborative Computational Project No. 4 |
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If imosflm breaks down on Windows Vista and Windows 7, disable Aero by following the instruction on this link:
http://www.howtogeek.com/howto/windows-vista/disable-aero-on-windows-vista\
There are links to instructions to enable Aero on the same page.
CCP4i will give an error message if you try to create or manipulate a project folder that is on a network drive mounted using a Samba server from a Linux system. This is due to permission settings on the mounted folder. In order for CCP4i to be able to write to the folder the permissions for the folder must be set so that "other" has write access. Use chmod to change the permissions for the folder on the Linux system.
Running a program that generates a harvest file fails with a message of the form:
The program run with command: refmac5 XYZIN "C:/D7_temp/52_warpNtrace_refmac9.pdb" XYZOUT "C:/Ccp4Temp/D7_1_4_2_pdb_1.tmp" HKLIN "C:/D7_temp/output_i212121_refmac23.mtz" HKLOUT "C:/Ccp4Temp/D7_1_4_3_mtz_1.tmp" LIBOUT "C:/D7_temp/D7_1_4_lib.cif" has failed with error message Last system error message: Unknown error Refmac_5.5.0102: Open failed: File: C:/D7_temp/DepositFiles/PROJECT/unknown191108:11:55:13.refmac
This occurs when the name given to the harvest files which includes ":". These characters can't be parsed correctly on windows installations. This usually happens when the initial dataset was processed with dstartrek or scalepack.
To get around the problem turn off the harvesting. Eg for refmac use the "run and view com file" option. In the list of keywords that it then presents enter a new keyword "NOHARVEST". Alternatively change the value for DNAME in the keyword list so it does not contain colons. The best remedy is to use the program CAD to change the Harvest file name (DNAME) in the MTZ file.
There is a problem with the executable scala.exe originally distributed with CCP4 6.3.0 causing incorrect formatting in the 'Summary data' output. Values for most lines of this table are reported as 0.000 or NaN. The scaled MTZ file is however correct. Users are advised either to replace scala.exe with the fixed version, linked to here.
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. Download the file from the following link and place it in $CCP4/bin replacing the original version of pointless.exe.
The input fixed model mode of molrep fails with the message:
Fortran runtime error: End of recordDownload the updated version of the molrep binary from the following link and replace the version in $CCP4/bin with this version.
Superpose executable produces pdb files with additional blank lines. Download the updated version of superpose binary from the following link and replace the version in $CCP4/bin with this version. (Also, an output of the ccp4-style operations is restored as it was in ccp4-6.1.13)
The scala and import tasks may fail with an error in ctruncate.exe . This occurs when the mtz history is empty. Download the file from the following link and place it in $CCP4/bin
Installation of a new task fails due to a missing TASK_MODULES,213 or 231 in modules.def. The work around is to edit C:\CCP4-Package\ccp4-6.1.13\ccp4i\etc\WINDOWS\modules.def to add the missing lines:
TASK,MODULE,213 programlist TASK,MODULE,231 programlist
This file is missing from the early versions of the 6.1.2 distribution. It should reside in $CCP4/lib/data. If it is missing you may see an error similar to the following from some of the programs:
>>>> CCIF signal CCIF_FOPEN (severity: SEVERE ERROR/FATAL) <<<<
(Raised in zzs_undump)
Cannot open file C:\CCP4-Packages\ccp4-6.1.2\lib\data\cif_mmdic.lib for reading!
Download the file from the following link and place it in $CCP4/lib/data
No CCP4i problems for CCP4 6.1.2 reported to date.
The seqwt program, which determines the molecular weight of a protein from
its sequence, is missing from the Windows distribution. The missing executable
can be downloaded from
ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/updates/seqwt.exe
and should be copied to the $CCP4/bin directory.
(Thanks to Nick Bauer)
Molrep fails with a file not found error (usually a .crd file) when run in multi-copy search mode. To fix this problem please
download the latest version of the Molrep executable and replace the one in your $CCP4/bin directory with it. The file is available from:
ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/updates/windows/molrep.exe
Buccaneer fails with an error message on windows machines. The job is listed as FAILED in the CCP4i job list window. A new executable
(cbuccaneer.exe) has been created which fixes this problem. Download it from the link given below and replace the 6.1.1 version in $CCP4/bin.
ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/updates/windows/cbuccaneer.exe
No CCP4i problems for CCP4 6.1.1 reported to date.
When loading a data set into iMosflm on Windows Vista machines the program crashes with an error message from the wish program reporting a realloc error. This is because the wish executable provided by CCP4 on windows has problems on Windows Vista machines. The workaround is to download and install the Active TCL distribution which is available from the Activestate website. Important: Download and install one of the 8.4.??? series distributions. The 8.5.??? versions do not come with all the components required for running iMosflm..
When you have ActiveTCL installed you will then have to edit the CCP4 configuration so that the ActiveTCL version of wish is used to start iMosflm from CCP4i. In the CCP4i GUI click on the "System Administration" button and select "Configure Interface". Find "Command to run iMosflm" and edit its value, replacing "wish" with "C:\Tcl\bin\wish". Note that this assumes that you have installed ActiveTCL under C:\Tcl. Restart the GUI for the new settings to take effect. iMosflm should now work.
When working with an mtz file containing a large number of reflections, Refmac may fail with a stack overflow or floating point overflow error message. This can be overcome by using the latest Refmac executable from the Prerelease page. Users who downloaded from the Prerelease page before 02/02/2009 will need to redownload.
(Thanks to Zhenbo Cao and Todd Talley)
No CCP4i problems for CCP4 6.1.0 reported to date.
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, which contains new versions of cad.exe, sortmtz.exe, scala.exe and scaleit.exe. These 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)
Sfall crashes on Windows Vista with a message similar to the following:
Can't open file C:\Ccp4Temp\\sfall_INTP1.05240
A fixed executable is available from:
ftp://ftp.ccp4.ac.uk/fr45/sfall.exe
Download this one and replace your existing version in $CCP4/bin.
(Thanks to John Helliwell)
One of the file references within the fft.script file is unquoted and therefore causes this failure when trying to make a map.
This problem can be fixed by doing the following
(Gary Hunter)
The findncs example in %CEXAM% (equivalent to $CEXAM/unix/runnable on unix based systems) gets stuck in an infinite loop in the refinement subroutine refrt in lgglib.f.
We noticed that in the current 5.0.2.1 release of windows version of CCP4 a file called cif_mmdic.lib was missing. This will cause failure with truncate and mlphare if data harvesting is enabled in the preferences in CCP4i.
Problem has now been addressed, you can update your 5.0.2.1 using this update
When running a program under windows, or a task using the CCP4 interface, the job may fail with the message 'No translation for logical name 'MMCIFDIC''. This is because during installation of the windows version of CCP4, the 'MMCIFDIC' environment variable has not been set. This needs to be set to the cif_mmdic.lib file which, under Windows, is located in the ccp4bin directory.
The fix is to set this environment variable manually. The way to set environment variables under Windows OS is as follows: Click 'Start' in the bottom left-hand corner of the screen. Select 'Settings' then 'Control Panel' and open up the 'System' icon.
Click the 'Advanced' tab and then open up 'Environment Variables'. There are 2 sets of variables - User variables and System Variables. Under System Variables, click 'New'. Enter 'MMCIFDIC' (in capital letters) for the 'Variable Name' and enter the full path of the cif_mmdic.lib file for the 'Variable Value'. Click 'OK' to finalise, then 'OK' again to set and leave the environment variables menu.
Clicking on molrep task gives: "Error: invalid command name HKLIN MAPIN CIFIN"
The problem is due to corrupted ccp4i files. Fixed files are available:
These need to replace the corresponding files wherever you unpacked CCP4.