[Chimera-users] CHIMERA script for CONSURF

Eric Pettersen pett at cgl.ucsf.edu
Thu Apr 17 11:24:16 PDT 2008

If the conservation scores are already in the b-factor field of the  
PDB, then you can skip the defattr part and use commands like:

	color red @/bfactor>3.0 & @/bfactor<=4.0

to color atoms.


On Apr 17, 2008, at 11:14 AM, Elaine Meng wrote:

> 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
> -----
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
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