[Chimera-users] ask for help about surface and Label color

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 8 12:52:46 PDT 2013

Hi Jian!
(1) Unfortunately molecular surface calculations fail for some structures because of numerical error.  There are several possible workarounds, described here:

I don't understand what you mean by "modify the structure" or why you would need the surface to do that, but if I didn't answer that part of the question, you can write back with more explanation.

(2) Yes, you can change label font/size and color labels separately from other things, either with the menu or with commands.  

Actually, for figures I usually recommend "2D Labels" instead of the regular labels.  These do not move with the structure, you just add them on top.  In that case you should figure out the exact view first and then place the 2D Labels.  In 2D Labels  (in menu under Tools… Utilities) you can specify the color, size, font, and contents of each label independently.  You can move each 2D label to wherever you like in the Chimera window. The 2D labels can include symbols, and you can also add arrows with that dialog.  Click the Help button on the dialog for more information, or see here:

For the regular labels (3D, that move along with the molecule), you can change font and fontsize but only for all of the 3D labels together.  That is done in the Preferences (under Favorites in the menu), category: Background.  However, their colors can be set individually either with the menu or the color command.  Menu: in Actions… Color, choose "all options…" and then in the resulting dialog you can choose the setting under "Coloring applies to" before choosing the color for the selected atoms (or just their labels, depending on what you chose).  If using the color command, include the ",l" modifier to mean labels only, or "rl" for residue labels only, or "al" for atom labels only, etc.  For example, command:

color hot pink,l sel

… to color the labels only of the selected atoms hot pink.  See the "color" command manual page:

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 Aug 8, 2013, at 12:19 PM, "Jian Guan" <jug25 at psu.edu> wrote:

> Hi,
> I am Jian, working in Hershey Medical Center, PSU. I am a Chimera User. I have two questions.
> 1: When I fit protein molecule structure into the density map of Virus particle. Showing the protein molecule in Surface is not allowed by Chimera. An error window popped out said: “surface calculation failed, mscalc returned code 2”. I wonder to know how to solve this problem. I want to modify the molecule structure after fitting.
> 2: When I label the selected residues, they are always with the same color with residues, can I set them separately? Can I edit the label font?
> Thank you so much.
> Hope to hear from you soon.
> Jian

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