[Chimera-users] CHIMERA script for CONSURF

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 17 11:14:19 PDT 2008

Hi Fabian,
I had failed to notice you are one of the ConSurf developers, so my  
reply focused more on what an outside user could do.  However, if you  
are thinking of providing Chimera scripts from the server, that would  
be great!!

If so, you probably do want discontinuous coloring with exactly the  
same colors and sets of residues, so that all the graphics programs  
would show the same thing.

Thus the Chimera script should contain "colordef" to define the  
colors and "color" to apply them to the residues.  There are  
different possibilities for specifying the residues in the color  
command, however.

(a) simply specify the residues by their residue numbers, like in the  
Consurf rasmol scripts

(b) use "alias" to name sets of residues and then specify the  
residues by the alias string

(c) make an attribute definition file (this file is read using the  
command "defattr") and then specify residues by attribute value.   
Disadvantage is an extra file.  Advantages are that the Chimera  
script could stay the same and only a new attribute definition file  
made for each structure, and that a user could later decide to use a  
different coloring scheme for the attribute.  Both the normalized  
score attribute and the 1-9 category score could be assigned in the  
same file.

I can provide more details on any of these if you would like.  Sorry  
about the length of the previous mail - I was trying to cover all the  
possibilities since I wasn't sure what you wanted!
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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