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>
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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 ...
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...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
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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@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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