[PyMOL] Pymol fab ss = 4 introduces bends in the structure

[Annemarie Honegger]

You get kinks wherever there is a proline in the sequence, because the ring of 
the PRO residues restrict the phi angle 

Annemarie

> 
> --
> 
> Message: 4
> Date: Fri, 7 Apr 2017 14:26:34 +0200
> From: Ahmad Abdelzaher <underoath...@gmail.com>
> Subject: [PyMOL] Pymol fab ss = 4 introduces bends in the structure
> To: pymol-users <pymol-users@lists.sourceforge.net>
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> 
> Hello,
> 
> I used cmd.fab('sequence', ss=4) to create 1baz_linear_protein.pdb,
> where sequence is the sequence extracted from 1baz.pdb.
> 
> My question is, why does Pymol introduce the bends that you can see in
> 1baz_linear_protein.pdb attached below?
> 
> Regards.
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Re: [PyMOL] Pymol fab ss = 4 introduces bends in the structure

[Tsjerk Wassenaar]

Hi Ahmad,

Because the chain contains prolines. These typically cause kinks in a chain.

Cheers,

Tsjerk

On Fri, Apr 7, 2017 at 2:26 PM, Ahmad Abdelzaher 
wrote:

> Hello,
>
> I used cmd.fab('sequence', ss=4) to create 1baz_linear_protein.pdb,
> where sequence is the sequence extracted from 1baz.pdb.
>
> My question is, why does Pymol introduce the bends that you can see in
> 1baz_linear_protein.pdb attached below?
>
> Regards.
>
> 
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> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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