[PyMOL] Can't build trans peptides ?

[R. Charbel MAROUN]

Hello Pymolers,

When trying to build a polypeptide chain with the Build Residue command, 
I find no "trans" conformation for the phi and psi angles, only Helix 
and Beta sheet. Is there a simple way of building a chain in the trans 
(extended) conformation ?

Thanks in advance.

-- 
R. Charbel MAROUN, Ph.D., H.D.R.
UMR-S INSERM U1204/UEVE
Structure et activité des biomolécules
normales et pathologiques
Université d'Evry-Val d'Essonne
Bâtiment Maupertuis
Rue du Père Jarlan
91000 EVRY
FRANCE
Tél: +33 1 69 47 76 64
FAX: +33 1 69 47 02 19
e-mail charbel.mar...@inserm.fr

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Re: [PyMOL] Can't build trans peptides ?

[Thomas Holder]

Hi Charbel,

After you opened the builder panel, you can change the "secondary_structure" 
setting to 4 before you start building:

PyMOL> set secondary_structure, 4

You may also like the "fab" command to build peptides:

http://pymolwiki.org/index.php/Fab

Extended poly-ALA example:

PyMOL> fab , ss=4

Cheers,
  Thomas

On 11 Feb 2016, at 06:48, R. Charbel MAROUN  wrote:

> Hello Pymolers,
> 
> When trying to build a polypeptide chain with the Build Residue command, 
> I find no "trans" conformation for the phi and psi angles, only Helix 
> and Beta sheet. Is there a simple way of building a chain in the trans 
> (extended) conformation ?
> 
> Thanks in advance.
> 
> -- 
> R. Charbel MAROUN, Ph.D., H.D.R.
> UMR-S INSERM U1204/UEVE
> Structure et activité des biomolécules
> normales et pathologiques
> Université d'Evry-Val d'Essonne
> Bâtiment Maupertuis
> Rue du Père Jarlan
> 91000 EVRY
> FRANCE
> Tél: +33 1 69 47 76 64
> FAX: +33 1 69 47 02 19
> e-mail charbel.mar...@inserm.fr

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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