[Chimera-users] building linker peptide

Eric Pettersen pett at cgl.ucsf.edu
Wed May 21 11:34:27 PDT 2008

Just deleting the SEQRES records _might_ be good enough.  Otherwise  
go with what Elaine wrote.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On May 21, 2008, at 9:59 AM, Elaine Meng wrote:

> 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 chain.
> 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
> renum
> 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,  
> however.
> Maybe someone else can think of a more elegant approach.
> Best,
> Elaine
> --------
> 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
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> <renum2.f>
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