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

Greg Couch gregc at cgl.ucsf.edu
Wed Jul 20 14:27:14 PDT 2011

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,


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)
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