[Chimera-users] make one chain from two chains ID in PDB

[Forbes J. Burkowski]

Hi:

On Tue, 2 Mar 2010, Elaine Meng wrote:

> I forgot to mention that when you change chain ID, you usually also
> need to change the residue numbering so that residues will be uniquely
> specifiable.  For example, if you have two residues both numbered 10
> in chain B, it may be difficult to do something to only one or the
> other in Chimera.  Those editing servers allow renumbering in addition
> to changing the chain ID.
> Elaine
>

Just a note:  If two chains are given the same chain ID, it is not clear
how everything will properly work out, even with renumbering.  I would
imagine that Chimera would see the last residue in the first original
chain as the part of a backbone that joins it to the first residue in the
second original chain.  Would this unfortunate connection occur?

Cheers,
Forbes




> On Mar 2, 2010, at 2:12 PM, Elaine Meng wrote:
>
> > Dear Jianbo,
> > You may want to try one of these PDB-editing web servers:
> >
> > <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi>
> >
> > <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>
> >
> > Both make you choose the file before you can see the options, but
> > can do several things, including changing chain ID and renumbering.
> > I haven't tried exactly what you describe, but it is probably worth
> > trying before using a text editor.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> > On Mar 2, 2010, at 1:35 PM, Dong, Jianbo wrote:
> >
> >> Hello,
> >>
> >> I'm working with a PDB file, in this file, one protein peptide was
> >> recognized as two chains (B and C), I want to make it as one chain,
> >> so
> >> it will be easier to do some interface analysis and modeling. I
> >> guess I
> >> can open the file as WORD file and change all the C to B one by
> >> one, but
> >> it's too much work to edit it that way.
> >>
> >> May I get some help for this? Is there a easier way to do this?
> >>
> >> Many thanks,
> >>
> >> Jianbo
> >
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