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@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