[chimera-dev] distance measurements

[Eric Pettersen]

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 at 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
> 
> -- 
> 
> 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
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