[Chimera-users] renumbering pdb

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 3 15:48:56 PDT 2008

Dear Sebastian,
Currently there is no way to change residue numbers in Chimera.  You  
would need to text-edit the PDB file (usually done with a script or  

I attached a little fortran program, renum2.f, that removes chain IDs  
and renumbers the residues sequentially starting with whatever number  
you tell it.  However, you may not be able to use it depending on  
your computing environment.  If you are on some unix-type computer  
with the "f77" compiler, you would just  compile it with something like:

f77 renum2.f -o renum

Then execute it with


It would ask for the names of the input and output PDB files and what  
residue number to start with.  However, if you can't use fortran  
programs or you don't want sequential numbering, you may need to use  
a text-editor or write your own script.
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. you can view the contents of renum2.f at
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On Jul 3, 2008, at 3:05 PM, bustik at gmx.net wrote:

> dear chimera-users,
> i am just starting to use chimera, so this will be a really simple  
> question to you (although i
> didn't find anything about this in the manual...):
> is there a simple command to change residue numbers in a pdb file  
> (i built up a homology
> model and want to elevate all residue numbers in the model the same  
> amount)?
> thanks in advance
> sebastian
> -- 
> Sebastian Kruggel
> Eppendorfer Weg 17d
> D 20259 Hamburg
> fon: +49 (0)40 4192 9579
> mobil: +49 (0)151 1789 2232
> e-mail: bustik at gmx.net

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