[Computational-biology] Re: Interpolate missing residues in pdb files

Linlin Yan via comp-bio%40net.bio.net (by yanlinlin82 from gmail.com)
Fri Jul 4 19:46:51 EST 2008


On Jul 4, 12:57 pm, "ozgun.harmanci" <ozgun.harma... from gmail.com> wrote:
> Hello,
> I am having trouuble with missing residues in pdb files and need to
> replace them (i.e. interpolate them) using a program. I think swiss-
> pdbviewer and pymol do that. My problem is that I am not very capable
> of using those programs and the person whom I asked for help told me
> that I have to check for missing residues in pdb file, open swiss-
> pdbviewer then add residue at correct place and finally she told me
> that I might need to do an energy minimization and I am thinking that
> I will definitely do a mistake there. I was wondering if anyone knows
> a more automated way to get the missing residues inserted for me
> because I am thinking that you can find missing residues in pdb and
> and programs can read that info and add these missing residues
> themselves automatically.. (but again maybe not..)
>
> Thanks.
>
> Sincerely,
> Arif.

Even if an automatic way to do that could be found, the theoretical
models used in the methods must be understood clearly. In addition,
all results from computation and/or software need be verified by
experiments, since they just give hints or guides for that.



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