problem with a script calculating distance between residues
Dear all, The script below has been validated for me by the Chimera team sometimes ago. In fact this script does not work each time I run it: When reaching the pdb dockSL0007.pdb, or dockSL0010.pdb, or dockSL0020.pdb,... Chimera can remained fixed on the current PDB file as if it faces problem to open it. I'm forced to close Chimera which does not respond anymore. The exit code is 805306369. I attached dockSL0009.pdb and dockSL0010.pdb. What can I do to report this bug (which may be due to something external to Chimera; my Chimera version is 1.5.2 Build 32411; my plateform is Windows 7 64 bits) since I have to brutally stop Chimera, and know more about this problem? Many thanks for your help Damien from chimera import runCommand as rc #from chimera.tkgui import saveReplyLog for i in range(1, 101): rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\dockSL%04d.pdb" % i) rc("distance :246.C@CB :297.A@CB") rc("distance :246.C@CB :297.B@CB") rc("close all") #rc("saveReplyLog('replyLog%04d.txt')" % i)
This is the first I've heard of this problem. You could try upgrading Chimera to verison 1.5.3, but I would be surprised if that helped. To learn more about where chimera is hanging, I'd recommend installing the Process Explorer program from http://technet.microsoft.com and the Windows SDK. Process Explorer is like the Task Manager, but lets you see partially inside the process, and the Windows SDK includes a debugger. The chimera binaries do not include debugging symbols, so the debugger is of limited utility, but you never know. Also, if you use Chimera's Help / Report a Bug dialog to submit this bug, it will tell us about your system configuration, and we might spot something you could easily fix. Bonne chance, Greg On 07/20/2011 03:50 AM, Damien Larivière wrote:
Dear all,
The script below has been validated for me by the Chimera team sometimes ago.
In fact this script does not work each time I run it: When reaching the pdb dockSL0007.pdb, or dockSL0010.pdb, or dockSL0020.pdb,... Chimera can remained fixed on the current PDB file as if it faces problem to open it. I'm forced to close Chimera which does not respond anymore. The exit code is 805306369. I attached dockSL0009.pdb and dockSL0010.pdb.
What can I do to report this bug (which may be due to something external to Chimera; my Chimera version is 1.5.2 Build 32411; my plateform is Windows 7 64 bits) since I have to brutally stop Chimera, and know more about this problem?
Many thanks for your help
Damien
from chimera import runCommand as rc #from chimera.tkgui import saveReplyLog for i in range(1, 101): rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\dockSL%04d.pdb" % i) rc("distance :246.C@CB :297.A@CB") rc("distance :246.C@CB :297.B@CB") rc("close all") #rc("saveReplyLog('replyLog%04d.txt')" % i)
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I don't have anything great to add, but you should check to make sure it isn't anything obvious. When Chimera hangs like this, is it using a very large amount of memory (use the Task Manager to see how much memory)? Is the disk it's writing to filling up? --Eric On Jul 20, 2011, at 2:27 PM, Greg Couch wrote:
This is the first I've heard of this problem. You could try upgrading Chimera to verison 1.5.3, but I would be surprised if that helped. To learn more about where chimera is hanging, I'd recommend installing the Process Explorer program from http://technet.microsoft.com and the Windows SDK. Process Explorer is like the Task Manager, but lets you see partially inside the process, and the Windows SDK includes a debugger. The chimera binaries do not include debugging symbols, so the debugger is of limited utility, but you never know. Also, if you use Chimera's Help / Report a Bug dialog to submit this bug, it will tell us about your system configuration, and we might spot something you could easily fix.
Bonne chance,
Greg
On 07/20/2011 03:50 AM, Damien Larivière wrote:
Dear all,
The script below has been validated for me by the Chimera team sometimes ago.
In fact this script does not work each time I run it: When reaching the pdb dockSL0007.pdb, or dockSL0010.pdb, or dockSL0020.pdb,... Chimera can remained fixed on the current PDB file as if it faces problem to open it. I'm forced to close Chimera which does not respond anymore. The exit code is 805306369. I attached dockSL0009.pdb and dockSL0010.pdb.
What can I do to report this bug (which may be due to something external to Chimera; my Chimera version is 1.5.2 Build 32411; my plateform is Windows 7 64 bits) since I have to brutally stop Chimera, and know more about this problem?
Many thanks for your help
Damien
from chimera import runCommand as rc #from chimera.tkgui import saveReplyLog for i in range(1, 101): rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\dockSL%04d.pdb" % i) rc("distance :246.C@CB :297.A@CB") rc("distance :246.C@CB :297.B@CB") rc("close all") #rc("saveReplyLog('replyLog%04d.txt')" % i)
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Damien Larivière -
Eric Pettersen -
Greg Couch