pymol-users

[PyMOL] conformational states in the mutagenesis wizard

[Xavier D. <Xav...@st...>]

Hi,

I've just realized that through the mutagenesis wizard you can 
view/select different conformations for a sidechain. I've been playing 
around, and it seems that the conformations are selected according to a 
backbone-independent rotamer library. Am I correct? Which library has 
been used?

I would also like to know if there is anybody out there using the 
rotamer toggle plugin. I've just installed it, and although it seems 
extremely useful, it makes PyMOL very slow to start. I'm running PyMOL 
0.98 for MacOSX in a PowerBook G4 1GHz with 1Gb of RAM (running MacOS X 
10.4.2)

Thanks in advance,

Xavier

-- 
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)

E-mail: Xav...@st...
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021

Re: [PyMOL] conformational states in the mutagenesis wizard

[Dan K. <dw...@ma...>]

Hey,
    The rotamer toggle script originally loaded the Dunbrack 
Backbone-Dependent rotamer library upon PyMOL startup.  However, I've 
changed it so that it will get loaded the first time you try to access 
the rotamer menu instead.  The code is fixed on www.PyMOLwiki.org .  Now 
PyMOL will start at regular speed. Thanks for the catching the 'bug' Xavier.

I beleive the mutagensis wizard in the newer ( > 0.98) will incorporate 
the Dunbrack library in some way or another.

~Dan Kulp

Xavier Deupi wrote:

> Hi,
>
> I've just realized that through the mutagenesis wizard you can 
> view/select different conformations for a sidechain. I've been playing 
> around, and it seems that the conformations are selected according to 
> a backbone-independent rotamer library. Am I correct? Which library 
> has been used?
>
> I would also like to know if there is anybody out there using the 
> rotamer toggle plugin. I've just installed it, and although it seems 
> extremely useful, it makes PyMOL very slow to start. I'm running PyMOL 
> 0.98 for MacOSX in a PowerBook G4 1GHz with 1Gb of RAM (running MacOS 
> X 10.4.2)
>
> Thanks in advance,
>
> Xavier
>


-- 
   Dan Kulp
   Biophysics Graduate Student @ UPenn
   dw...@ma...
   http://dwkulp.homelinux.net/tiki/tiki-index.php
--