Re: [PyMOL] (no subject)

[Vivien S. <viv...@gm...>]

This worked! Thank you Leandro and Jed!

 

From: je...@gm... [mailto:je...@gm...] On Behalf Of Jed Goldstone
Sent: Tuesday, April 4, 2017 11:35
To: Vivien Schoonenberg <viv...@gm...>
Cc: pym...@li...
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 <viv...@gm... <mailto: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
Redfield 3-52 MS #32
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http://www.whoi.edu/hpb/Site.do?id=481
(508) 685-2253 (cell/home)     (508) 289-4823 (work/WHOI)