Hai oteri, I tried the way you had suggested but still i get some error. chimera comes with its own python and i dnt know if there is a clash. Could you please write me why this ImportError happens. [cbala@RAMANA ~]$ export PYTHONPATH=/usr/local/chimera_15/lib:/usr/local/chimera_15/share:$PYTHONPATH [cbala@RAMANA ~]$ export LD_LIBRARY=/usr/local/chimera_15/lib:$LD_LIBRARY [cbala@RAMANA ~]$ 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 chimera Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/PIL/__init__.py", line 15, in <module>
ImportError: libgfxinfo.so: cannot open shared object file: No such file or directory --------------------------------------------------------------------------------------------------------------------- On Tue, May 18, 2010 at 1:39 PM, francesco oteri <francesco.oteri@gmail.com>wrote:
Dear bala, to invoke chimera as a python module ( Question 2) you should execute the following steps:
1) Finding the root directory of the chimera installation (example:/usr/local/chimera ) 2) export LD_LIBRARY=/usr/local/chimera/lib:$LD_LIBRARY 3) export PYTHONPATH=/usr/local/chimera/lib:/usr/local/chimera/share:$PYTHONPATH
The result is:
oteri@priestley:~$ python Python 2.6.4 (r264:75706, Dec 7 2009, 18:43:55) [GCC 4.4.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
import chimera
2010/5/18 Bala subramanian <bala.biophysics@gmail.com>
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.
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
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.
4)What is the syntax to change the color of pseudobonds ?
*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
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-- Cordiali saluti, Dr.Oteri Francesco