[Chimera-users] Questions about homology modelling

[Elaine Meng]

Hi Jim,
You can color by any attribute, once it is assigned.  New attributes  
will be listed in the Render by Attribute (coloring) tool.  You can  
create attributes arbitrarily with Define Attribute, as mentioned,  
and various different tools in Chimera create tool-specific attributes:

(1) A "charge" attribute could be created by reading in a Mol2 file  
with charges or by running the Add Charge tool (an example of use is  
included in the Attributes tutorial).  This uses Cornell et al. AMBER  
charges for standard residues and calculates charges for nonstandard  
residues with Antechamber.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/ 
addcharge.html

You could use Attribute Calculator to create a residue attribute from  
those atom attributes, or if you used the Define Attribute approach,  
you could define the residue charge directly.  That would be quite  
simple to do for the standard amino acids, for example.

(2) Electrostatic potential:  Currently Chimera does not calculate  
the potential for you, but reads several formats of maps.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp

If you have opened an electrostatic potential map and a structure,  
you can use the "Values at Atom Positions" tool to create an atom  
attribute of the potential value at its position.  This can be used  
with other kinds of maps as well, such as electron density.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/ 
density.html

Alternatively, you could color a surface directly by potential or  
density without going through atomic attributes.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ 
surfcolor.html

(3) Docking scores:  the ViewDock tool automatically assigns whatever  
DOCK scores are in the ligand file as attributes.

(4) Residue conservation:  if you have a sequence alignment and  
associated structure(s) open in Chimera, the structure residues get  
various conservation attributes according to the columns in the  
alignment.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
multalignviewer/framemav.html
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
multalignviewer/multalignviewer.html#mavAttributes

There are probably additional examples, but that may already be more  
than you wanted to know.

I would be happy to provide more specific assistance with whatever  
you would like to do - let me know,
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




On Jan 15, 2008, at 12:01 PM, Nicholson, Jim wrote:

> Elaine:
>
> Thanks for the reply.  My comment about coloring refers to using a  
> table
> of residue hydrophobic index to color atoms or surfaces.  I used it  
> all
> the time for docking.  I also want to color things by residue  
> charge or
> electrostatic field.  Most modelling packages offer something like  
> that,
> and, I couldn't find it in Chimera, so, I thought would ask.
>
> -Jim Nicholson
>