Re: two chain in pdb file

From: Edelmiro Moman (moman_at_titus.u-strasbg.fr)
Date: Tue Aug 01 2006 - 03:40:12 CDT

Hi Dhiraj,

I would recommend you to try to model the missing chains in prior to run
psfgen.

If all the backbone atoms are there and only a few side chains are
missing, you can open your pdb file with Deepview (Swiss PDB viewer,
which is free and compatible with most systems) and it will add the
missing side chains for you. That may be fair enough for "unimportant"
residues.

However, from your message, it seems that backbone atoms are also
missing, in which case you might want to do some homology modelling to
"reconstruct" the missing region. There are a number of free homology
modelling programs (Modeller) and servers (SwissMODEL) that you can use
for that purpose. However, as your missing region will quite likely be a
"disordered" loop you might be interested in using specific tools for
loop modelling. There are a few avaliable (some of them are web-based
servers) and I am sure you can easily find them by searching in Google.
Modeller is also good for that (there is a tutorial on loop refinement
in the Modeller website that you may find useful).

Miro

Dhiraj Srivastava wrote:

> Hi all
> i want to simulate my protein whose pdb file has although only
> one chain but in vmd it looks like 2 chain as coordinates of some
> amino acid residues are missing. should i consider it as one chain or
> two? what about the patches at the end of the chain?
>
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153

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