[Chimera-users] display of single letter AA code?

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 28 10:45:51 PDT 2004

Hi Mark,
	The answer is "yes, but not automatically".  First, you can use the 
selection inspector to change atom labels to anything you want (start 
the selection inspector either via the button in the lower right-hand 
corner of the Chimera window or with Tools->Inspectors->Selection 
Inspector).  Note than for non-wireframe depictions you may need to add 
spaces to the start of the label to get it clear of the atom radius 
[this behavior will be much improved in the next release (in about a 
week)].  Not a great solution if you're doing this repeatedly of 
	Another alternative is to make a relatively minor change to the Python 
source code.  If you are using release 1.1951, then you can edit <where 
you installed chimera>/share/chimera/tkgui.py to make the change.  Line 
1314 of that file will look like this:

	rl = r.type

you can change it to look like this:

	from resCode import res3to1
	rl = res3to1(r.type)

You need to preserve the original indentation, which is significant to 
Python.  With this change, labels created from the Actions menu will 
use single-letter residue codes.  It has the drawback that ligands and 
so forth will have 'X' as the residue label.  I can provide a slightly 
more sophisticated code change to avoid 'X' labels if you'd like.  
Also, on a Mac, you are going to have to use Terminal to get into the 
Chimera app package, and the path will be <where you installed 

So my question to you is whether this labeling is something you want to 
do on a day-to-day basis, or is it something you are doing just for an 
image or so infrequently that using the selection inspector is "good 
enough".  Further, if we made single-letter labeling an option, would 
you want an exception made for ligands and/or non-standard residues?

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Sep 27, 2004, at 8:01 PM, Mark Daniels wrote:

> Hello Chimera administrator(s)-
>   I was wondering if there is any way fior Chimera to display amino 
> acid residue names in single-letter format, rather than the 
> three-letter format one gets when selecting 
> Actions-->Label-->residue-->name ?  I have looked over all the 
> documentation I can but have not found anything to answer this 
> question.
> Thanks in advance-
> Mark
> Mark J Daniels
> Department of Cell Biology
> The Scripps Research Institute
> La Jolla, CA   92037
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> Chimera-users at cgl.ucsf.edu
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