Subject: Re: [modeller_usage] Hang/crash on clustering
From: Modeller Caretaker <>
Date: Sun, 27 Apr 2008 09:54:26 -0700
James Irving wrote:
I'm using Modeller 9v3 (Linux) and 9v1 (WindowsXP). I perform a
rudimentary automodel with the script below. On both systems I get 200
output models, all of which appear to have an identical number of
residues and atoms, however the script just hangs when it executes the
How long did you leave the script running? Many parts of Modeller are
computationally expensive, and can run for half an hour or more without
producing any output.
I've then used the clustering script found at
http://salilab.org/modeller/wiki/Cluster_PDBs with the 200 models, which
uses transfer_xyz. This time the script ends with a segmentation fault
(Linux) or closes unexpectedly (Windows XP). There are are no errors
reported in the log file in either instance, it simply executes fine up
to the point where clustering is requested and gets no further.
As this hasn't been mentioned before I assume it's not a bug.
On the contrary, a segmentation fault is *always* a bug. Thanks for
bringing it to my attention. Could you send me (not the list) your full
input files (e.g. alignments, PDBs, etc.) so that I can reproduce and
fix your two problems?