Hi all,<br>I&#39;m using Modeller 9v3 (Linux) and 9v1 (WindowsXP).&nbsp; I perform a rudimentary automodel with the script below.&nbsp; 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.<br>
<br>----------------<br># Homology modeling by the automodel class<br>from modeller import *&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>from modeller.automodel import *&nbsp; <br><br>log.verbose()&nbsp;&nbsp;&nbsp; <br>env = environ()&nbsp; <br><br># directories for input atom files<br>
env.io.atom_files_directory = &#39;./&#39;<br><br>a = automodel(env,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; alnfile&nbsp; = &#39;sequences3.pir&#39;,&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; knowns&nbsp;&nbsp; = (&#39;prot1&#39;,&#39;prot2&#39;,&#39;prot3&#39;),&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; sequence = &#39;protx&#39;,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; assess_methods = (assess.GA341, assess.DOPE))&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>a.starting_model= 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>a.ending_model&nbsp; = 200&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
a.make()&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br><br>a.cluster()<br>-----------------<br><br>I&#39;ve then used the clustering script found at <a href="http://salilab.org/modeller/wiki/Cluster_PDBs">http://salilab.org/modeller/wiki/Cluster_PDBs</a> with the 200 models, which uses transfer_xyz.&nbsp; This time the script ends with a segmentation fault (Linux) or closes unexpectedly (Windows XP).&nbsp; 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.<br>
<br>As this hasn&#39;t been mentioned before I assume it&#39;s not a bug.&nbsp; Has anyone else had this problem and overcome it?<br><br>Thanks!<br>James<br><br>