[Biopython] Adding SEQRES to a pdb structure

[Peter Cock]

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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