[Chimera-users] Questions about homology modelling

Eric Pettersen pett at cgl.ucsf.edu
Tue Jan 15 12:38:32 PST 2008

Hi Jim,
	Chimera also has a built-in residue hydrophobicity attribute  
("kdHydrophobicity") available in the Render by Attribute tool that  
you can use to color structures/surfaces.


On Jan 15, 2008, at 12:25 PM, Elaine Meng wrote:

> 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
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