[Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 6 09:34:33 PST 2017


The message is saying that Chimera does not know what kind of file “xz.batch” is.  If it is a Chimera command file it should be named ending with .cmd or .com, and if it is a Python file, it should be named ending with .py 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command>

Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Dec 6, 2017, at 6:02 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> Elaine,
> 
> the question was related not to the bash script for this routine but
> instead to the input file for the batch chimera.
> 
> E.g. I have indentified the following command which works in command
> line of Chimera GUI. It finds the contacts between chain A and others
> and save the outputs to the log file in the same dir.
> 
> findclash :.a test other overlapCutoff -3.0 intraMol false saveFile
> ./test_cont.log
> 
> Now when I had put the same line into the input.batch and executed it
> with the batch_chimera, i have recieved the following error message
> from python:
> 
> chimera_batch ./rep2.pdb ./xz.batch
> Opening rep2.pdb..
> Traceback (most recent call last):
>  File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimeraInit.py",
> line 708, in init
>    chimera.openModels.open(a, prefixableType=1)
>  File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py",
> line 1916, in open
>    raise ValueError, "Unknown model type"
> ValueError: Unknown model type
> 
> Error while processing ./xz.batch:
> ValueError: Unknown model type
> 
>  File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py",
> line 1916, in open
>    raise ValueError, "Unknown model type"
> 
> See reply log for Python traceback.
> 
> does it the problems with the python variables? In my *.bashrc file I
> have sourced the pathways to both chimeras in the following manner:
> 
> export PATH=$PATH:/home/t-iris2-011/.local/UCSF-Chimera64-1.12/bin:/home/t-iris2-011/.local/UCSF-Chimera64-batch/bin
> 
> James






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