[Biopython] Adding SEQRES to a pdb structure

[Ahmad Abdelzaher]

Thanks for the replies. Removing the seqres does affects chimera's display
of the sequence. I can do it manually for now, but it's obviously a pain.
Maybe I can write a python script from scratch and share it with you.

Regards.

On Tue, Feb 20, 2018 at 4:56 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Hi Ahmad,
>
> I am not a protein structure expert, but your plan sounds
> sensible (removing part of the sequence both in the SEQRES
> header and in the coordinate section).
>
> Biopython's PDB parsing is very focused on the coordinates
> section, with quite limited support for the header part. I've
> never tried editing the header myself.
>
> Not ideal, but if this is one file, you can probably do this by hand?
>
> Peter
>
> On Mon, Feb 19, 2018 at 4:35 PM, Ahmad Abdelzaher
> <underoath006 at gmail.com> wrote:
> > Hello everyone,
> >
> > First I want to explain what I'm doing  to make sure I will accomplish
> what
> > I want to do using what I'm trying to do. My main question, of course,
> is if
> > I can do it using Biopython, and how.
> >
> > I have two structures of Tubulin homologs. One (unmodelled) has the loop
> > from Q35 to K60 unmodeled. The loop is still shown when I open the
> sequence
> > in Chimera. The other one has the same loop modelled.
> >
> > Upon inspection of the two pdb's in a text editor, the unmodelled
> structure
> > has a block with a header called "SEQRES". I'm guessing that's where
> Chimera
> > gets the sequence from (see picture)?
> >
> > Now the question, is can I create and add a SEQRES block to the modelled
> > structure and then delete the loop coordinates? Would that accomplish
> what
> > I'm trying to do? How can I do it in Biopython?
> >
> > Regards.
> >
> >
> >
> > _______________________________________________
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>
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