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