[Chimera-users] Recursive structure matching and acquisition of descriptive numbers

Greg Couch gregc at cgl.ucsf.edu
Wed Sep 7 11:49:19 PDT 2016


Yes, Chimera's Python code is only "warrantied" to work with its own 
Python.  See question 3b of the Chimera Programming FAQ, 
https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b, for 
how to install other software into Chimera.  Other parts of the FAQ may 
help you too.


That said, Jaime Rodríguez-Guerra took my previous comments on this 
subject, 
http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html, 
and came up with pychimera, https://pypi.python.org/pypi/pychimera. I 
haven't checked to see how it handles all of my caveats, and it can't 
completely without using a modified Python, but I suspect that it would 
be good enough for you.


     HTH,


     Greg


On 09/07/2016 07:36 AM, Healey, Joe wrote:
>
> Hi Eric,
>
>
> That looks good thank you. I think I'm going about this slightly the 
> wrong way after some investigation however.
>
>
> Am I right in thinking that chimera can't be imported in to python 
> inside a normal bash shell, and rather it must be done the other way 
> round? So file manipulation and such must be done by calls to the 
> system from within the chimera python shell, rather than a python 
> interpreter calling chimera modules in?
>
>
> It certainly makes the chimera steps I plan to do much easier, but I 
> was going to include it in a pipeline with some other programs and it 
> makes that a little more taxing (though not insurmountable!).
>
>
> Additionally, I plan to invoke this inside a script on a headless 
> linux box (hence why running it through a python script was ideal), so 
> whatever solution I use will need to be 'command line friendly'.
>
>
> In effect all I need is the actual algorithm for the matching process 
> to be accessed somehow from a python script.
>
>
> Do you have any advice about how best to proceed?
>
>
> Many thanks,
>
>
> Joe Healey
>
>
> M.Sc. B.Sc. (Hons)
> PhD Student
> MOAC CDT, Senate House
> University of Warwick
> Coventry
> CV47AL
> Mob: +44 (0) 7536 042620  | Email: J.R.J.Healey at warwick.ac.uk
>
> Jointly working in:
> Waterfield Lab 
> <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> 
> (WMS Microbiology and Infection Unit)
> and the Gibson Lab 
> <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick 
> Chemistry)
>
> Twitter: @JRJHealey <https://twitter.com/JRJHealey>  | Website: MOAC 
> Page 
> <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
>
>
> ------------------------------------------------------------------------
> *From:* Eric Pettersen <pett at cgl.ucsf.edu>
> *Sent:* 31 August 2016 18:23
> *To:* Healey, Joe
> *Cc:* chimera-users at cgl.ucsf.edu
> *Subject:* Re: [Chimera-users] Recursive structure matching and 
> acquisition of descriptive numbers
> Hi Joe,
> This old chimera-users post has a Python script attachment that 
> demonstrates how to call the underlying MatchMaker function to get the 
> RMSD value programmatically.  The mailing list gives the attachment a 
> “.bin” extension but it’s really a .py file.  Just change the 
> extension if you need to.  Let me know if you have any questions about 
> how to adapt the script to your needs…
>
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>> On Aug 31, 2016, at 3:02 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk 
>> <mailto:J.R.J.Healey at warwick.ac.uk>> wrote:
>>
>> Hi,
>>
>> I have several hundred structure simulations that were performed on 
>> our HPC resource. Each simulation has approximately 5 models 
>> associated with it. I also have HMM model homologies for each of 
>> these proteins.
>>
>> I would like to use chimera's matchmaker function to compare the 
>> simulated structured to their nearest 'real' counterpart with a 
>> resolved structure. In order to do this I plan to script chimera to 
>> pull in the simulated models as well as the near homolog and then run 
>> the matchmaker algorithm.
>>
>> My question is: can the RMSD value that is returned in the reply log 
>> be 'accessed directly' such that for each match that is performed, I 
>> can obtain the RMSD and thus a ranking for the best fitting 
>> structures - or will it require parsing the reply log?
>>
>> Thanks
>>
>> Joe Healey
>>
>>
>> M.Sc. B.Sc. (Hons)
>> PhD Student
>> MOAC CDT, Senate House
>> University of Warwick
>> Coventry
>> CV47AL
>> Mob: +44 (0) 7536 042620  | Email:J.R.J.Healey at warwick.ac.uk 
>> <mailto:J.R.J.Healey at warwick.ac.uk>
>>
>> Jointly working in:
>> Waterfield Lab 
>> <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/>(WMS 
>> Microbiology and Infection Unit)
>> and the Gibson Lab 
>> <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick 
>> Chemistry)
>>
>> Twitter:@JRJHealey <https://twitter.com/JRJHealey>  | Website:MOAC 
>> Page 
>> <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
>> _______________________________________________
>> Chimera-users mailing list:Chimera-users at cgl.ucsf.edu 
>> <mailto:Chimera-users at cgl.ucsf.edu>
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>
>
>
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