[Chimera-users] weighted distance

Elaine Meng meng at cgl.ucsf.edu
Wed May 5 10:28:35 PDT 2010

Hi Bala,
If these were atom-associated values, you could make your own custom  
attribute and then easily color or scale the atoms by the values.   
However, these are values associated with distance measurements, and  
we don't have a similarly nice mechanism for assigning attributes to  
bonds or pseudobonds.

Another point is that all pseudobonds in a group (such as all distance  
monitors) have the same linewidth.  Instead of different linewidths,  
you could show them with different colors and/or as sticks of  
different widths.

With Chimera commands, you can create a distance monitor and set its  
stick thickness, color, etc.:
open 1zik
alias pair1 #0:22.a at oe2:25 at 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.

Another possibility instead of making distance monitors is to make  
custom pseudobonds with the Pseudobond Reader tool, which reads a file  
with lines like:

#0:22.a at oe2:25 at ne hot pink


but that does not get you any farther than the distance monitor  
approach, as you would still need to conditionally set color (which  
can be done in the input file) or radius (with "setattr" as above)  
depending on the distance.
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 5, 2010, at 7:29 AM, Bala subramanian wrote:

> Dear Friends,
> Is there any way to display weighted distance in chimera. For  
> example, in the attached data file, we have distance in column 1 and  
> its corresponding importance in column 2. What i would like to do is  
> to load the structure, display the distance between two group of  
> residues and adjust the width of the line (created by distance  
> monitor) according to the importance of the distance in the data file.
> Thank you,
> Baa
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