[Chimera-users] clustering of docking solutions

Sebastian Kruggel kruggel at chemie.uni-hamburg.de
Tue Nov 18 02:23:38 PST 2008

Hi Elaine,

thanks for the ideas - indeed it seems to be the simplest way to write a 
small python script to loop over the ligands and use the rmsd command 
(indeed I'm interested in the RMSD values as they are and no best-fit). 
The examples I found in the mailing list were command scripts - if I use 
python (to get better possibilities to loop etc), how do I combine for 
instance the rmsd command in the script?

for i in os.system('./'):
   rmsd #1.1 #1.i

gives syntax error - of course because of the python/chimera mixture... 
But how can I combine these two correctly?
Sorry for these basic quesions...

Best regards

Sebastian Kruggel
Institut für Pharmazie
Bundesstr. 45 | Raum 112
D 20146 Hamburg
Tel +49(0) 40 42838 3626

Elaine Meng schrieb:
> Hi Sebastian,
> Are all the docked structures the same molecule, just in different 
> positions?
> You are right that ViewDock doesn't have clustering, and Ensemble 
> Cluster automatically determines the clusters without allowing you to 
> specify an RMSD cutoff.
> My ideas only pertain if the structures are all the same molecule or 
> at least contain a common set of atoms:
> (a) You could use Ensemble Match to compare the ensemble to itself, if 
> the atoms in common have the same names.  This would not perform 
> clustering, but it calculates all-by-all RMSD values using a set of 
> atoms you specify.  However, these are best-fit RMSDs of the 
> structures, while I suspect you may want the RMSDs in their current 
> positions instead.  Another caveat is that it creates a dialog that is 
> an N x N table, which may not be manageable for a large number of 
> structures (high N).
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblematch/ensemblematch.html> 
> There is an example of using Ensemble Match at the end of the "model 
> panel and ensembles" tutorial:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html> 
> (b) As you mentioned, you could convert to a multi-model PDB, and use 
> the MD Movie tool's RMSD analysis to calculate an all-by-all RMSD 
> map.  However, it would require more work to extract the RMSD values 
> (output is a grayscale map) and these are also best-fit RMSDs.  This 
> option is more practical for high N than option (a), however.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> 
> Part 2 of the "trajectories/ensembles" tutorial includes an example of 
> MD Movie RMSD Analysis:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part2> 
> (c) You could use a script to do all-by-all comparisons of the 
> structures with the "rmsd" command.  This calculates current-position 
> RMSDs rather than best-fit RMSDs.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
> See these previous posts for more general information on scripts:
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003261.html> 
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003262.html> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> On Nov 17, 2008, at 6:07 AM, Sebastian Kruggel wrote:
>> Hi all,
>> I am looking for a possibility to cluster docking results (multimol2
>> file) in chimera. In DockView I can't find such tool and in the
>> EnsembleCluster method I don't see a way to set rmsd limits.
>> I found a hint to the MD Analysis tool in the mailing list, ok, I could
>> convert my docking solutions into pdbs and use this, but probably there
>> is another simple and convenient way that I am just too blind to see ;-)
>> Maybe somebody can help?
>> Thanks in advance,
>> Sebastian

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