[Chimera-users] Offsetting residue numbering

sette at uniroma2.it sette at uniroma2.it
Tue Mar 22 11:32:16 PDT 2011

Or try here



Def. Quota "Elaine Meng" <meng at cgl.ucsf.edu>:

> Hi Sumitro,
> I would renumber the residues in the input file before opening it in  
> Chimera.  Of course, manual editing is too tedious.  One of these  
> web servers for PDB editing may be the most convenient:
> <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi>
> <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>
> Uh-oh,  the second one is unreachable currently.  I'm hoping it's  
> temporary... but at least the first one is still there.
> I believe they both make you choose or upload the file before you  
> can see the options, but can  do several things, including changing  
> chain ID and renumbering the residues.
> 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 Mar 22, 2011, at 6:33 AM, Sumitro Harjanto wrote:
>> Hi Elaine,
>> Is there a way to introduce a systematic offset to the residue  
>> numbering in a model?
>> The numbering in my model is different from the convention. Eg. the  
>> methionine that's supposedly in position 5 is labeled as MET 4,  
>> alanine in position 6 as ALA 5, and so on. I can't do it manually  
>> cos there are many residues. Is there an easy way to resolve this  
>> other than using a script to automatically assign the labels? It'll  
>> be good if i can resolve this from the root , such that my atom  
>> specification is also consistent with the naming convention I use. :)
>> Cheers,
>> Sumitro
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Dr.Marco Sette, Ph.D.

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