[Chimera-users] building linker peptide

[Fabian Glaser]

Dear Elaine and Eric,

Elaine program worked beautifully, and it's in any case better to have a 
renumbered PDB,

Thanks a lot!!

Fabian

Eric Pettersen said the following on 21/05/08 21:34:
> Just deleting the SEQRES records _might_ be good enough.  Otherwise go 
> with what Elaine wrote.
>
> --Eric
>
>                         Eric Pettersen
>
>                         UCSF Computer Graphics Lab
>
>                         http://www.cgl.ucsf.edu
>
>
> 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 
>> <mailto: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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>

-- 
Fabian Glaser, PhD

Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL

Web:   http://bku.technion.ac.il
Email: fglaser at tx.technion.ac.il
Tel:   +972-(0)4-8293701
Cel:   +972-(0)54-4772396