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

[Stoilova-McPhie, Svetla]

Hi David,

I am not feeling good at all today and would like to get a sick day tomorrow if this is OK with you.

The Arctica autoloader part arrived today and the FEI engineers will replace and test the equipment. Once they replace the part it may take up to two days for the column to pump down.

Either way I will be first thing on Friday to check with them.

I will put the request in people soft shortly.

Best,

Svetla





________________________________
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, December 6, 2017 12:40 PM
To: James Starlight
Cc: Chimera BB
Subject: Re: [Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models

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>
findclash - rbvi.ucsf.edu<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
www.rbvi.ucsf.edu
Chimera Commands Index Usage: findclash atom-spec options Usage: ~findclash. Findclash identifies interatomic clashes and contacts based on VDW radii and user ...



...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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