[Chimera-users] building linker peptide
fglaser at technion.ac.il
Thu May 22 05:56:59 PDT 2008
Dear Elaine and Eric,
Elaine program worked beautifully, and it's in any case better to have a
Thanks a lot!!
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 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
>>> 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
>> <mailto:meng at cgl.ucsf.edu>
>> UCSF Computer Graphics Lab and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
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
Email: fglaser at tx.technion.ac.il
More information about the Chimera-users