[Chimera-users] atomic fluctuations

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 22 10:39:59 PDT 2009

On Apr 22, 2009, at 10:26 AM, Bala subramanian wrote:

> Dear Elaine and Pett,
> Greetings. I have a matrix of atomic fluctuations, is it possible to
> map it on to the structure using chimera. Say i would prefer to color
> differently all atoms having a fluctuation of more than a threshold.
> Similarly if i give a matrix of correlations, i should color
> differently those atoms which are highly correlated.
> Thanks,
> Bala

Dear Bala,
To do this you would create an "attribute assignment file" (a simple  
text format) with the values and read it in with Define Attribute (or  
command "defattr").   That will assign the values to your structure as  
an "attribute."

Then you can show the values of your new attribute with colors, etc.,  
and select atoms based on those values, and use them in command-line  
specifications, just like any other attributes (bfactor,  
kdHydrophobicity, etc.).

This is exactly what you need for the fluctuation values.  Showing the  
correlation would be more complicated, because attributes are  
properties of atoms and not atom pairs.  You could assign each "row"  
of your correlation matrix as a different attribute with a different  

Define Attribute and the concept of "attributes":

Attribute assignment file format:

Render/Select by Attribute:

Please send questions about Chimera to chimera-users at cgl.ucsf.edu and  
not to our personal addresses, unless you are sending private data or  
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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