[Chimera-users] Labelling helices

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 19 09:51:21 PDT 2011

Hi George,
There isn't a way to do that directly.  Although residues are automatically assigned as being in helix 1, strand 1, helix 2, strand 2, etc. there isn't a simple way to show one label per secondary structural element.

You can easily specify the residues in that element, for example helix 2:

select helix & :/ssId=2

...or strand 3:

color yellow strand & :/ssId=3

You could color-code the secondary structure elements in this manner.

If this is for a figure, you would have to use 2D Labels.  These labels just go in the 2D plane and do not move along with your structure, so you would add them last, after putting the structure in the exact position you want for your figure.  2D Labels can be text, symbols, and arrows.  The 2D Labels tool is in the menu under Tools... Utilities.

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 Oct 19, 2011, at 4:13 AM, George Tzotzos wrote:

> I've been looking at the documentation to find a way to number (label) protein helices. Perhaps I didn't use the right keywords so I didn't find anything helpful.
> What I would like to do is give ascending numbers to individual protein helices starting from the aminoacid terminus onwards.
> Any suggestions will be greatly appreciated.
> Regards
> George

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