On Feb 4, 2011, at 2:51 AM, Julien wrote:
Hi Elaine, I would like to find clashes between a ligand and a protein. I have around 100 000 poses of this ligands. The information to get the poses are at the moment saved in a pdb file. Indeed three pseudo atoms are used to place the ligand in the correct position using the command match.
The workflow would be the followin: open ligand open protein open pseudo.pdb
match ligand position1 findclash match ligand position2 ...
First, this is very slow, even in batch mode. Maybe you know a better way to do that. Second chimera does not open more than 9999 residues, the pseudo pdb have nearly 100 000 residues. Is there a way to get around that.
I guess the routine findclash calculates all distances brutally and compare them to a threshold. many greetings Julien
Hi Julien, Findclash does calculate distances between atom centers, but the cutoff parameter is compared to "overlap" between the VDW spheres -- in other words, smaller atoms must be closer together than larger atoms to be considered overlapping or clashing. The output information (optional) includes both the center-center distances and the overlaps, however. You can limit the calculation to only certain atoms. There are also options to control cutoff and other settings. Details are here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> If you are really just using "findclash" without arguments, that would look at the whole structure and take more time than necessary. For example, if your ligand is model #0 and the protein model #1, one way to limit the calculation to only clashes between them and send info to the Reply Log is: findclash #0 test #1 log true Otherwise, I'm not an expert on any large-scale calculations or how you might optimize the procedure for large sets of atoms, so I'm CC-ing this question to the chimera-users list. (It is generally better to send Chimera questions to this list rather than to me personally.) The other users or developers may have good ideas. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco