Hi Feixia, You could certainly use Chimera to do that. You need to know some Python. Take a look at the Programmer’s Guide: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> In particular, the “basic primer” discusses how to loop over files in a directory and do things to them one by one. Here’s some example code for printing the lysine CA-CA distances for a single open file. You could take that and move it into the loop described in the basic primer — customizing it as you wish… from chimera import openModels, Molecule # opening NMR files can produce multiple models, so use a loop... for mol in openModels.list(modelTypes=[Molecule]): lysCas = [a for a in mol.atoms if a.name == “CA” and a.residue.type == “LYS”] for i, ca1 in enumerate(lysCas): for ca2 in lysCas[i+1:]: print mol.name, ca1, ca2, ca1.coord().distance(ca2.coord()) —Eric Eric Pettersen UCSF Computer Graphics Lab
On Aug 18, 2015, at 8:36 AM, Feixia <feixia.chu@unh.edu> wrote:
Hi there,
I am interested in retrieving distance information from large dataset in an automatic fashion. For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries. Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time. I wonder if we can do that with Chimera. Your advice will be highly appreciated.
Best, Feixia
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Feixia Chu, Ph.D. Associate Professor Molecular, Cellular & Biomedical Sciences University of New Hampshire Gregg Hall, Rm436 35 Colovos Rd Durham, NH 03824 Tel 603 862 2436 _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev