[Chimera-users] Selective surface colouring of aminoacids by hand

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 22 09:56:24 PST 2011

Hi Heinrich,
There are several different ways to accomplish this.  There are two basic parts to the task, indicating the residues you want to color, and coloring just the molecular surface for those residues and not the atoms/bonds/ribbons.

If using the command line, you can do it all in a single command, for example:

color hot pink,s #0:5,67,577-580

the ",s" part means molecular surface only, and there is a specification syntax for describing what atoms or residues you want to affect with your command.  #0 means model zero (you could have several different files open, thus different models, and only want to color residues in the first model).  If you only had one model with those residue numbers, you could omit the #0 part.  The colon : means residues.  The example would affect the given residue numbers in all chains, but if you only wanted those in chain A, you could use 5.a,67.a,577-580.a instead of just the numbers.  Command-line specification is powerful and can be done in many ways.  What I described here is "hierarchical" specification:
as used in the command "color"

Or, if you don't want to use commands, you can do it by first selecting the residues and then using the Actions... Color dialog.
(A) selecting the residues.  Again there are several ways to do it, but one is to show the sequence (choose menu item Favorites... Sequence) and in that sequence window, drag a box around the desired residues to select them.  If you want to select several residues that are not adjacent, just use Shift while dragging the second, third, etc. boxes.  
(B) coloring the residues.  From the menu, choose Actions... Color... all options to show the coloring dialog.  In that dialog, change "Coloring applies to" to "surfaces" and then click the desired color.  (Afterward you may want to change back to "all of the above" to avoid later confusion.)

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 22, 2011, at 12:23 AM, Heinrich Lünsdorf wrote:

> To whom it may concern.
> Dear colleagues,
> I am a novice in working with Chimera and a practicing electron microscopist. I learned to fit X-ray model data into EM-densities.
> My special question acutally is to select several surface exposed aminoacids by hand (either as a sequence ' aa #x to #y' or single aa '#5,67,577,579' etc.) as they have been epitope-mapped by antibodies and colorize them uniquely in the "MSMS main surface" mode of Chimera. How to colorize at the 'ribbon' I know already but I need this selective colorization at the 'Actions --> Surface --> Solid' level. How can I do this?
> Thank you coridally for your help in advance.
> Heinrich Lünsdorf

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