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

Eric Pettersen pett at cgl.ucsf.edu
Wed Aug 31 10:23:29 PDT 2016

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 <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html>


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Aug 31, 2016, at 3:02 AM, Healey, Joe <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>_______________________________________________
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