[Chimera-users] Questions about homology modelling
pett at cgl.ucsf.edu
Tue Jan 15 12:38:32 PST 2008
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
> (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.
> 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.
> 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.
> Alternatively, you could color a surface directly by potential or
> density without going through atomic attributes.
> (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
> 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 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
> On Jan 15, 2008, at 12:01 PM, Nicholson, Jim wrote:
>> Thanks for the reply. My comment about coloring refers to using a
>> of residue hydrophobic index to color atoms or surfaces. I used it
>> the time for docking. I also want to color things by residue
>> charge or
>> electrostatic field. Most modelling packages offer something like
>> and, I couldn't find it in Chimera, so, I thought would ask.
>> -Jim Nicholson
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