[Chimera-users] problem with a script calculating distance between residues

Eric Pettersen pett at cgl.ucsf.edu
Wed Jul 20 14:32:12 PDT 2011

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?


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 at CB :297.A at CB")
>>     rc("distance :246.C at CB :297.B at CB")
>>     rc("close all")
>>     #rc("saveReplyLog('replyLog%04d.txt')" % i)
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20110720/511bef7b/attachment.html>

More information about the Chimera-users mailing list