Hi Vincent, Thanks for the encouragement! (a) Coloring by ViewDock score: Currently you cannot color the docked compounds based on values in the ViewDock table (except manually/individually), but that is a very good idea. It sounds like the values in each numerical column should be assigned as model attributes to the docked compounds. Then you could just use the Render by Attribute tool to define a color mapping, as can be done now for other attributes. We will need to do similar things in the future for scores/energies/probabilities of modeled structures, modeled loops, and sidechain rotamers when related features are added to Chimera. I mainly deal with the user interface and do not know if there are any difficult implementation issues, but this is definitely a good feature to put on the "to do" list. (b) Coloring "key": We haven't thought much about providing a key for the color mapping, but there was another similar request recently. Another thing to consider. Thanks for your suggestions, Elaine On Aug 4, 2006, at 1:58 AM, Vincent Zoete wrote:
Hi,
Does it exist a way to color the different ligand positions obtained during a docking run, and displayed by the Viewdock module of chimera, as a function of a given energy term present in the columns of the viewdock table? If not, I think this could be an useful option to add to chimera. Also, it could be interesting to have the possibility to display the color scale as a function of the energy term together with the structures. If it cannot be done in the chimera display, it could be in the generated figures.
Otherwise, congratulation for the great job the UCSF computer graphics lab is making with Chimera!
Thank you for your time. Sincerely, Vincent
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- 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