This worked! Thank you Leandro and Jed!
From: [email protected] [mailto:[email protected]] On Behalf Of Jed Goldstone
Sent: Tuesday, April 4, 2017 11:35
To: Vivien Schoonenberg <[email protected]>
Cc: [email protected]
Subject: Re: [PyMOL] (no subject)
Try using
remove not alt +A
to remove alternative conformations.
Jed
On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg
<[email protected] <mailto:[email protected]> > 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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