[Chimera-users] Problem running Modellerfrom Chimera (versión 1.11.2(build 41380) 2016-12-05 19:45 UTC. Platform Linux64)

[Eric Pettersen]

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 at 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
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