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
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open d:\result\pdb\1B0G.pdb
open d:\result\pdb\1DUZ.pdb
match #0:1-9.C@ca #1:1-9.C@ca
match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o
match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca
match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o
close #1
open d:\result\pdb\1EEY.pdb
match #0:1-9.C@ca #1:1-9.C@ca
match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o
match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca
match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o
close #1
open d:\result\pdb\1EEZ.pdb
match #0:1-9.C@ca #1:1-9.C@ca
match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o
match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca
match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o
close #1
open d:\result\pdb\1HHG.pdb
match #0:1-9.C@ca #1:1-9.C@ca
match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o
match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca
match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o
close #1
open d:\result\pdb\1HHI.pdb
match #0:1-9.C@ca #1:1-9.C@ca
match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o
match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca
match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o
close #1
…
…
…
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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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