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 > cluster command.
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?
Ben Webb, Modeller Caretaker