[Chimera-users] How can I calculate RMSD with chimera script

[Michał Kadlof]

Thank you :)

2015-05-19 21:52 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:

> Since runCommand() doesn't return any value, you need to call the
> underlying Python rmsd() function, which isn't hard to do.  Somewhere at
> the top of your script put:
>
> from Midas import rmsd
>
> and then replace:
>
> rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k))
>
> with:
>
> val = rmsd("#0:{0}-{1}".format(s,k), "#1:{0}-{1}".format(s,k))
>
> --Eric
>
> On May 19, 2015, at 12:45 PM, Michał Kadlof <ramidas at gmail.com> wrote:
>
> Yes it work, but then I have to write and run another script to parse
> output from chimera which cost HDD access time. I was wonder, if it
> possible to do it in single script without dumping output to separate file.
>
> --
> Michał
>
> 2015-05-19 18:53 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>
>> Hi Michał,
>> Redirecting output from a program into a file is pretty easy in any
>> Unix/Linux shell.  This would redirect Chimera's non-error output into a
>> file named "chimera-output.txt":
>>
>> chimera *chimera-arguments-you-normally-use* > chimera-output.txt
>>
>> You can also redirect the error output, but the syntax for that depends
>> on the shell you are using.  You should be able to easily Google it if you
>> need to do that.
>>
>> --Eric
>>
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu
>>
>> On May 19, 2015, at 1:16 AM, Michał Kadlof <ramidas at gmail.com> wrote:
>>
>> Hello,
>>
>> I have a need of calculating about 1000 of RMSDs between two particular
>> regions of reference model and testing model. I would like to do this with
>> chimera script. I'm using chimera-1.10.1-Headless Linux 64-bit and have no
>> access to any GUI.
>>
>> Currently my script looks like this:
>>
>> import sys, os, re
>> from chimera import runCommand as rc
>>
>> << not important stuff >>
>>
>> rc("open %s" % (native))
>> for i in models:
>>     rc("open " + i)
>>     rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k))
>>     rc("close #1")
>>
>> rc("close all")
>> rc("stop now")
>>
>> This allow me to see output on the screen, but I don't know how to
>> capture it for further processing. I found somewhere something like this:
>>
>> from chimera.tkgui import saveReplyLog
>> << do something >>
>> saveReplyLog('replyLog.txt')
>>
>> But it seem to work only in versions with GUI.
>>
>> Please help.
>>
>> --
>> best whishes
>> Michał Kadlof
>>
>> University of Warsaw
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>> Chimera-users at cgl.ucsf.edu
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>>
>>
>>
>>
>>
>
>
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