[Chimera-users] building linker peptide

Elaine Meng meng at cgl.ucsf.edu
Wed May 21 09:59:48 PDT 2008

On May 21, 2008, at 1:29 AM, Fabian Glaser wrote:
> Another question regarding this issue, I succeded to make a new  
> bond and minimize it between two chains, A and B, in the same pdb.  
> But this created apparently a problem with the residue numbering  
> and Nterm recognition, since when I tried to add an additional  
> linker to the chimera I created, I got the following error message:
> "No MMTK name for atom "H" in standard residue ALA"
> I suspect that this is related to the fact that I still have two  
> chains, and Chimera does not identified the new bond, or something  
> similar.
> Is there a way to automatically rename the newly unified chains?
> Any suggetion will be highly appreciated.

Hi Fabian,
There is no automatic way to change chain ID.  Only the ugly manual  
text-editing way, sorry!  I guess that the ATOM part of the file no  
longer agreed with the SEQRES part of the file.

It might work to simply delete that atom, if it looks like it is extra.

However, I would probably go back to a PDB file saved after you added  
all your linker residues and edit it to remove all the lines except  
the coordinates (the ATOM and HETATM lines), remove the chain IDs,  
and renumber all the residues.  It is necessary to renumber the  
residues because there may be residues with the same number in the  
different chains, and now there would be no way to tell them apart  
(for example, two different residues numbered 10, which used to be  
residue 10 in A and residue 10 in B).   Unfortunately you will lose  
the ability to use the "familiar" residue numbering within the second  

I attached a fortran (f77) program to do this editing, but I realize  
you may not be able to use it depending on your computing  
environment.  If you are on some unix-type computer 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.

Then you would have to do the addh/addcharge/minimization stuff  
again, sorry.  I think it would already have the bond you wanted,  

Maybe someone else can think of a more elegant approach.
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

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