Thank you, Eric! I am still downloading PDB files through Bio.python. I am just interested in the overall distance distribution of residues, say Lys alpha carbon. NMR entries might end up over-representing due to their multiple models. Thank you for pointing it out. Is there a quick way to distinguish crystal structures from NMR structures? Best, Feixia On Wed, 19 Aug 2015 14:17:35 -0400, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
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
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