Dear Eric and Elaine, thanks very much, the bfactor + rangecolor - option works for me and Elaine's points might come in handy at a later point in time. Best, Christian On 09/16/2010 08:38 PM, Elaine Meng wrote:
Hi Christian, I would only add a couple of points to Eric's suggestion to use the "bfactor" attribute. These may or may not be relevant to your situation:
(1) Coloring by attribute is particularly nice for continuous-valued things, because they can be mapped to continuous gradations of color. I can't tell whether you want continuous coloring (e.g. red gradually shading to blue from one value to another) or discrete (e.g. exactly red for one group, exactly blue for another group). In the Render by Attribute tool, your value distribution will be shown in a histogram. One way to achieve discrete coloring would be to bracket each value with two thresholds (the vertical colored sliders that define the color mapping on the histogram) of the same color. Or, you could use commands something like
color hot pink @/bfactor=1 color orange @/bfactor=2
(2) Attributes could also be assigned with a separate input file, instead of the PDB file. It is a simple tab-separated column format, description and examples here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...>
That allows assigning multiple different attributes without having to make more PDB files. These attributes can be of different value types (float, integer, boolean, color, character string), they can be named anything you want instead of just bfactor, and if they are floating-point numbers of high precision you can use more digits than are available in the bfactor field in standard PDB format. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 16, 2010, at 11:08 AM, Eric Pettersen wrote:
Hi Christian, I'm happy you like Chimera enough to mis-use in in this way! :-) However, I don't think "rainbow" is the way to go here. Rainbow only affects connected strings of residues. For example, if you rainbow a protein system, waters and ligands will retain their original colors (and for your system, Chimera really has no way of knowing that your "residues" aren't peptide ligands). SInce you are creating your own PDB files anyway, what I suggest is that your put your "grouping info" into the bfactor field. Then you can use the Render by Attribute tool (or the rangecolor command) to color your points based on their bfactor.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>
--- Christian Schudoma, M.Sc. Ph.D. Student Bioinformatics Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 (331) 567-8624 email: schudoma@mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de