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

James Starlight jmsstarlight at gmail.com
Thu Dec 7 06:54:16 PST 2017


Thank you, Elaine!

One question: where the Reply Log will be saved after execution of the
batch chimera, assuming that I'am using cmd script without python?

# this is chimera.cmd"
findclash :.${i} test other overlapCutoff -3.0 intraMol false saveFile
 log true"


Thank you!


James

2017-12-06 18:40 GMT+01:00 Elaine Meng <meng at cgl.ucsf.edu>:
> Instead of saving to a log file with each command (which is better if you want a different file each time), save to the Reply Log with “findclash” option “log true”:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
> ...and then at the end, after multiple calculations, save the Reply Log to a file.  You could save it “manually”, menu Favorites… Reply Log, and then use the Save button on the Reply Log, or save it with python in the script as described at the bottom of this page:
> <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
>
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Dec 6, 2017, at 6:37 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>
>> P.S. is it possible to make a complex task script for batch chimera
>> e.g to find contacts between all of the chains and other atoms in the
>> sequential manner adding the results within the same log?
>>
>> # an example of such workflow within one batch input file for the batch chimera
>> findclash :.a test other overlapCutoff -3.0 intraMol false saveFile
>> ./test_cont.log
>> findclash :.b test other overlapCutoff -3.0 intraMol false saveFile
>> ./test_cont.log
>> ...
>> findclash :.p test other overlapCutoff -3.0 intraMol false saveFile
>> ./test_cont.log
>



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