[Chimera-users] error running large iterative script (return code 3)

[Eric Pettersen]

Hi Sumitro,
	I was unable to reproduce your error.  I used 98 models on my Mac  
(9506 pairs) without problem, and 39 models on an XP machine here in  
the lab and they both worked fine.  I asked about your version because  
the error message ("CloneMenu failed inside of MenuAddOrInsert") is  
mildly suggestive that it's a problem rebuilding one of the dynamic  
menus (e.g. Chain menu or Residue menu) as models are opened and  
closed, and we fixed a problem with that a few versions back.
	Nonetheless my best guess is that the problem is still something  
along those lines, so my suggestion would be to just open all 39 files  
and do the matching between pairs without constantly opening and  
closing structures.  I have attached a Python script that will go  
through all pairs of open models and run the "match" commands you were  
using.  Perhaps you can use the script as is or modify it to suit your  
purposes.  You run it (once you've opened your models) simply by  
opening it with File...Open or with the "open" command.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On Dec 14, 2009, at 10:33 PM, Sumitro Harjanto wrote:

> Hi,
>
> I was trying to run the following script (below), which calculates  
> RMSDs between 39 pdb models. Total iteration will be 741 with about  
> 3000 match commands. After it has run for about 10 mins chimera will  
> crash with an error: Chimera failed abnormally; the exit code was 3.  
> I've printed the debug lines below the script:
>
> Any suggestions..?
>
> Cheers,
>
> Sumitro
>
> --------------------------------------------------------
>
> open d:\result\pdb\1B0G.pdb
>
> open d:\result\pdb\1DUZ.pdb
>
> match #0:1-9.C at ca #1:1-9.C at ca
>
> match #0:1-9.C at n,ca,c,o #1:1-9.C at n,ca,c,o
>
> match #0:1-2.C,8-9.C at ca #1:1-2.C,8-9.C at ca
>
> match #0:1-2.C,8-9.C at n,ca,c,o #1:1-2.C,8-9.C at n,ca,c,o
>
> close #1
>
> open d:\result\pdb\1EEY.pdb
>
> match #0:1-9.C at ca #1:1-9.C at ca
>
> match #0:1-9.C at n,ca,c,o #1:1-9.C at n,ca,c,o
>
> match #0:1-2.C,8-9.C at ca #1:1-2.C,8-9.C at ca
>
> match #0:1-2.C,8-9.C at n,ca,c,o #1:1-2.C,8-9.C at n,ca,c,o
>
> close #1
>
> open d:\result\pdb\1EEZ.pdb
>
> match #0:1-9.C at ca #1:1-9.C at ca
>
> match #0:1-9.C at n,ca,c,o #1:1-9.C at n,ca,c,o
>
> match #0:1-2.C,8-9.C at ca #1:1-2.C,8-9.C at ca
>
> match #0:1-2.C,8-9.C at n,ca,c,o #1:1-2.C,8-9.C at n,ca,c,o
>
> close #1
>
> open d:\result\pdb\1HHG.pdb
>
> match #0:1-9.C at ca #1:1-9.C at ca
>
> match #0:1-9.C at n,ca,c,o #1:1-9.C at n,ca,c,o
>
> match #0:1-2.C,8-9.C at ca #1:1-2.C,8-9.C at ca
>
> match #0:1-2.C,8-9.C at n,ca,c,o #1:1-2.C,8-9.C at n,ca,c,o
>
> close #1
>
> open d:\result\pdb\1HHI.pdb
>
> match #0:1-9.C at ca #1:1-9.C at ca
>
> match #0:1-9.C at n,ca,c,o #1:1-9.C at n,ca,c,o
>
> match #0:1-2.C,8-9.C at ca #1:1-2.C,8-9.C at ca
>
> match #0:1-2.C,8-9.C at n,ca,c,o #1:1-2.C,8-9.C at n,ca,c,o
>
> close #1
>
> …
>
> …
>
> …
>
> --------------------------------------------------------
>
> initializing general preferences
>
> loading Tix
>
> initializing graphics
>
> create application
>
> loading Pmw
>
> creating main window
>
> creating menus
>
> creating toolbar
>
> creating viewer
>
> initializing OpenGL
>
> initializing preferences
>
> initializing dialogs
>
> initializing COM
>
> initializing extensions
>
> CloneMenu failed inside of MenuAddOrInsert.
>
> This application has requested the Runtime to terminate it in an  
> unusual way.
>
> Please contact the application's support team for more information.
>
> Return code: 3
>
> Press return or enter to to exit
>
>
> --------------------------------------------------------
>
>
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> Chimera-users at cgl.ucsf.edu
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