Hi Bala, On May 18, 2010, at 2:04 AM, Bala subramanian wrote:
Dear Eric and Elaine,
Thank you so much for your inputs. I could implement the 'weighted distance' representation. I have certain queries. I would appreciate your inputs for the same.
1) When i type help(object) in chimera's python shell, it shows the help message, is there any to way to make the help information to be displayed in a separate window. I tried in config setting but i couldnt make it.
I don't know of any way to make help() output go elsewhere.
2) Is there any way to invoke chimera within normal python interpreter. I am able to do this for pymol. But i dnt know if i can do the same with chimera. I tried to set PYTHONPATH, but it vain.
[cbala@RAMANA ~]$ python Python 2.5.2 (r252:60911, Sep 30 2008, 15:41:38) [GCC 4.3.2 20080917 (Red Hat 4.3.2-4)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
import pymol
Francesco's reply seemed like the right approach.
3) In the following code, i am collecting Cbeta atoms from two groups of residues and calculating the cb-cb distance. If instead of Cbeta, i have to calculate the side chain COM-COM (center of mass) distance between two groups of residues, how can i do it or which module should i use.
The general approach I would use is to: 3a) gather the residues' atoms 3b) screen out all hydrogens (since it will be tricky to eliminate only main-chain hydrogens due to possible variant naming schemes) 3c) screen out main-chain heavy atoms 3d) compute center of mass If one of the groups of residues was named 'rg1', then something like this: atoms = [a for r in rg1 for a in r] heavys = [a for a in atoms if a.element.number > 1] sides = [a for a in heavys if a.name not in ['C', 'CA', 'N', 'O', 'OXT']] from chimera import Point com = Point([a.xformCoord() for a in sides], [a.element.mass for a in sides]) If you had computed 'com1' and 'com2', then the distance would be: com1.distance(com2)
4)What is the syntax to change the color of pseudobonds ?
You assign a Color object to the pseudobond's 'color' attribute. If you know the colors' red, green, blue, and alpha (opacity) values (each in the range 0-1), you could get a Color object with: from chimera import MaterialColor color = MaterialColor(r, g, b, a) If you know the color name you'd like to use, then: from chimera.colorTable import getColorByName color = getColorByName("spring green")
I am pasting the script below so that it may be useful to someone who wants to do a similar thing.
import chimera from StructMeasure.DistMonitor import *
model=chimera.openModels.open('trial.pdb') res=model[0].residues don_atom=[];acp_atom=[]
#collecting CB atoms of donor and acceptor residues
for x in res: if x.type in ['ARG','GLN']: don_atom.append(x.atomsMap['CB'][0]) elif x.type=='GLU': acp_atom.append(x.atomsMap['CB'][0]) else: continue
#open the distance weight data
weight={} for line in open('rad.dat'): line=line.split() weight[float(line[0])]=line[1]
b=[] #pseudo bond list
for v1 in don_atom: for v2 in acp_atom: b.append(distanceMonitor.newPseudoBond(v1,v2))
#changing pseudo bond features
for pb in b: pb.drawMode=1 chi=round(pb.length()) if chi in weight: pb.radius=float(weight[chi])
Thanks, Bala
On Mon, May 10, 2010 at 8:07 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: Oops. The module name is "StructMeasure", not "StructureMeasure", so the correct line of Python would be:
from StructMeasure.DistMonitor import distanceMonitor
--Eric
On May 10, 2010, at 3:36 AM, Bala subramanian wrote:
Dear Elaine and Eric, Thanks for the inputs. I started the chimera interface and tried to use the StructureMeasure module using the IDLE that is present in chimera but it shows me import Error. I dnt understand why. I am using chimera 1.5 alpha version 29904. Do i need to set some path to use the module.
from StructureMeasure import * Traceback (most recent call last): File "<pyshell#8>", line 1, in <module> from StructureMeasure import * ImportError: No module named StructureMeasure
Bala
On Wed, May 5, 2010 at 8:37 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: On May 5, 2010, at 10:28 AM, Elaine Meng wrote:
With Chimera commands, you can create a distance monitor and set its stick thickness, color, etc.: open 1zik alias pair1 #0:22.a@oe2:25@ne dist pair1 setattr p drawMode 1 pair1 setattr p radius .05 pair1 setattr p color hot pink pair1 setattr p label " " pair1
However, it sounds like python will be necessary to conditionally set radius or color depending on the value of the distance.
A little more info on this possibility. You can get the distance- monitor pseudobond group in Chimera with:
from StructureMeasure.DistMonitor import distanceMonitor
and run through the distance-monitor pseudobonds with:
for pb in distanceMonitor.pseudoBonds: ...do something that sets pb.radius based on pb.length()...
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu