Re: [PyMOL] Creating PDB files from Primary Sequence

[Joel T. <joe...@ot...>]

Hi James,

Sounds like you want a homology model type set up, ie generate 
coordinates based on a template. Modeller can do this and an easier way 
is via the  swissmodel

http://swissmodel.expasy.org//SWISS-MODEL.html

If however you want a relatively random structure then pymol _can_ do 
this. Click on builder (top right og GUI) and then select protein. From 
here you can generate any sequence you want. You can then export this 
and use the program of your choice to run dynamics etc

Hope this helps

J

James R. Graham wrote:

> Hello,
>
> This may be slightly off-topic, but I was wondering whether PyMol  
> would allow one to enter a peptide sequence (generally short in  
> length) to create a template structure that can then be used for  
> structural refinements (minimizations, etc.) elsewhere.
>
> If PyMol cannot do this, is anyone aware of any program (preferably  
> Mac OS X or linux compatible) that would be able to do this?
>
> Any info would be greatly appreciated.
>
> And apologies if this question is too far off-topic.
>
> Regards,
> james
>
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034