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 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/ensem...>

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.ht...>

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#pa...>

(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@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