[Chimera-users] custom residue label

Sasha Tkachev stkachev at cellsignal.com
Mon Jun 20 08:26:04 PDT 2011

Hi Elaine,

Yes it definitely helps, thanks!


On Jun 17, 2011, at 5:20 PM, Elaine Meng wrote:

> Hi Sasha,
> If "programatically" includes Chimera commands, you could use a  
> command something like:
> setattr r label "Lys-57" :656.e
> Non-programatically, it can also be done by selecting the residue  
> and then using the menu (Actions... Label... residue... custom).
> I don't know python, so if that is what you meant, somebody else  
> will have to answer.
> However, you might just want to edit the PDB file in the first place  
> to avoid the bother.  You could text-edit it "manually" or use one  
> of these handy PDB-editing web servers:
> <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi>
> <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>
> <http://www.canoz.com/sdh/renumberpdbchain.pl>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jun 17, 2011, at 1:49 PM, Sasha Tkachev wrote:
>> How to programmatically set a residue label to an arbitrary text,  
>> e.g.
>> to say something like:
>> rlabel :656.E "Lys-57"
>> What happens in some structures, like for instance 1U35 structure  
>> that
>> contains H3 proteins, is that residue numbers in a PDB file is
>> different from residue number of the sequence. In this particular
>> example Lys57 of H3 on chain E maps to PDB residue number 656. So  
>> if I
>> use default labeling I am getting wrong results...
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