Re: [PyMOL] (no subject)

[Jed G. <jgo...@wh...>]

Try using

remove not alt +A

to remove alternative conformations.

Jed

On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg <
viv...@gm...> wrote:

> Hi there,
>
>
>
> I’m saving the sequences from each chain of the PDB via pymol with
>
> >>save something.fasta, chain A
>
>
>
> This is the same sequence that is shown in pymol and seems to correspond
> to the structure I am looking at.
>
> However, when I loaded new B-factors in my structure, I noticed something
> funny happened. The list which I made corresponding to the sequence I saved
> earlier was too short.
>
> I  found out by iterating that some residues repeated themselves(>>iterate
> (chain A and n. CA), print resn). They carry the same residue number, and
> are not shown in the sequence. However, when I load my B-factors my list
> shifts because of these repeats, making it too short for the complete chain
> and loading the wrong value onto residues.
>
>
>
> Does anyone know why this happens and how I can fix this?
>
>
>
> Thank you,
>
> Vivien
>
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-- 
-------------------------
Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
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