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. --Eric 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@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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