Hi,
You probably have a pdb file which has multiple possible conformations
for some residues. You can check this by visual inspection of such
residues. They have two side chains coming from the same CA. In the text
file you can see the conformations marked as A and B in the residue name
field, e.g. APHE BPHE.
If that is the case, you have to choose one of them either manually or
with some other molecular modeling software, e.g. gromacs.
I hope it helps!
Regards,
Leandro
On Mon, Apr 3, 2017 at 5:47 PM, 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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