Thanks Thomas!

Those scripts works fine. Could you tell me if there any way to install all of those scripts as the pymol plugins ( that I need not to load this scripts every time when I sttart pymol de novo )?


James


2011/11/23 James Starlight <jmsstarlight@gmail.com>
Thanks thomas

Those scripts works fine. Could you tell me if there any way to install all of those scripts as the pymol plugins ( that I need not to load this scripts every time when I sttart pymol de novo )?


James


2011/11/23 Thomas Holder <speleo3@users.sourceforge.net>
Hi James,

check this PyMOLWiki page: http://pymolwiki.org/index.php/Fab

However, the "fab" command does not take user defined phi/psi angles, only 4 predefined conformations ("ss" argument). User defined phi/psi can be handled by these scripts:

http://pymolwiki.org/index.php/CreateSecondaryStructure
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/#model

Cheers,
 Thomas

James Starlight wrote, On 11/23/11 11:43:

Dear PyMol Users!

I wounder to know about possible ways of creation of the peptide structures via PyMol Builder module. In particular I need create a linear structure of my protein ( with fixed phi and psi angles) for futher folding molecular dynamics simulation of that peptide. But in builder module I found only helix and sheet conformations for each aa. residue. How I can specify desired values for both torsion angles ?

Also I'd like to know is there any module for pymol wich could be used for obtaining linear unfolded structure for the defined sequence or folded protein ( in pdb) ?

Thanks,


James

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen