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

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 7 09:49:50 PST 2017


There is no “saveFile” in the command.  “log true” is a separate option that only means to show information in the Reply Log without saving any file. Please see the description of all the findclash options in the manpage:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

Then, AFTER all the calculations, you would save the Reply Log contents to a file either manually or with python, as explained in my previous message.

Elaine

> On Dec 7, 2017, at 6:54 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> 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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