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? —Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 21, 2018, at 3:43 PM, Sergio Garay <sergio.alberto.garay@gmail.com> wrote:
Hi all
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:
Model 0 (model1.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. seq (len 437): added target (len 437): model1.pdb (#0) chain A seq (len 437): model1.pdb (#0) chain A target (len 437): added Target seq: added Template structures: model1.pdb (#0) Run locally, the Modeller binary location: /usr/bin/mod9.19 Now, modeller is running locally... Wrote /tmp/tmp73g3JY/template_struc/model1.pdb_0_0.pdb MODELLER process output ----------------------- ----------------------- MODELLER process errors ----------------------- Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback
The problem seems to be that Chimera can not load the models obtained. I can find the model inside the directory: /tmp/tmp73g3JY/template_struc/model1.pdb_0_0.pdb
Thank you in advance.
Sergio
-- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users