<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">From the output, it looks like Modeller failed in a non-graceful way (i.e. crash). Try going to /tmp/tmp73g3JY and running "/usr/bin/mod9.19 ModellerModelling.py:. What happens?<div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><br class=""></div><div><blockquote type="cite" class=""><div class="">On Apr 21, 2018, at 3:43 PM, Sergio Garay <<a href="mailto:sergio.alberto.garay@gmail.com" class="">sergio.alberto.garay@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-size:small">Hi all</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">I've tried to run Modeller locally from Chimera (versión 1.11.2(build 41380) 2016-12-05 19:45 UTC. Platform Linux64. Windowing system: x11), but when it finishes, the model is not loaded inside Chimera. The log window give me the following output: </div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default"><div class="gmail_default"><i class=""><font size="1" class="">Model 0 (model1.pdb) appears to be a protein without secondary structure assignments.</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Automatically computing assignments using 'ksdssp' and parameter values:</font></i></div><div class="gmail_default"><i class=""><font size="1" class=""> energy cutoff -0.5</font></i></div><div class="gmail_default"><i class=""><font size="1" class=""> minimum helix length 3</font></i></div><div class="gmail_default"><i class=""><font size="1" class=""> minimum strand length 3</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Use command 'help ksdssp' for more information.</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">seq (len 437): added</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">target (len 437): model1.pdb (#0) chain A</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">seq (len 437): model1.pdb (#0) chain A</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">target (len 437): added</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Target seq: added</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Template structures: </font></i></div><div class="gmail_default"><i class=""><font size="1" class=""><span style="white-space:pre" class=""> </span>model1.pdb (#0)</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Run locally, the Modeller binary location: /usr/bin/mod9.19</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Now, modeller is running locally...</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Wrote /tmp/tmp73g3JY/template_struc/model1.pdb_0_0.pdb</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">MODELLER process output</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">-----------------------</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">-----------------------</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">MODELLER process errors</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">-----------------------</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Could not find platform independent libraries <prefix></font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Could not find platform dependent libraries <exec_prefix></font></i></div><div class="gmail_default"><i class=""><font size="1" class="">Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]</font></i></div><div class="gmail_default"><i class=""><font size="1" class="">'import site' failed; use -v for traceback</font></i></div></div><div class="gmail_default" style="font-size:small"><i class=""><br class=""></i></div>The problem seems to be that Chimera can not load the models obtained<div class="gmail_default" style="font-size:small;display:inline">. I</div> can find <div class="gmail_default" style="font-size:small;display:inline">the model</div> inside the directory: /tmp/tmp73g3JY/template_struc/<b class="">model1.pdb_0_0.pdb</b><div class="gmail_default"><br class=""></div><div class="gmail_default" style="font-size:small">Thank you in advance.</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">Sergio</div><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><font color="#0000ff" size="1" class=""><i class="">Sergio Garay<br class="">Dr. en Ciencias Biológicas<br class="">Facultad de Bioquimica y Cs. Biológicas<br class="">Universidad Nacional del Litoral<br class="">Santa Fe - Argentina<br class="">C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA<br class="">Argentina<br class="">Ph. +54 (342) 4575-213<br class="">Fax. +54 (342) 4575-221 </i></font></div></div></div>
</div>
_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>