Try using
remove not alt +A
to remove alternative conformations.
Jed
On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg <
vivienschoonenb...@gmail.com> 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
Redfield 3-52 MS #32
Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
(508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI)
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