[Chimera-users] Coloring binding modes according to an energy term with ViewDock

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 4 07:56:17 PDT 2006

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 

Thanks for your suggestions,

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
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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

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