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