Hi James.

Look here for windows:
http://www.pymolwiki.org/index.php/Windows_Install#Pre-compiled_PyMOL
Basically:

You can make a "pymolrc.pym" file, and put it under "C:\Users\YOU". In the file you can write the following listed. This folder is now in your PyMOL search path, so you can put pymol wiki scripts here. Note the forward slashes "/".


import sys
sys.path.append("C:/Python27/PyMOL/scripts")
Then put all scripts here, and write in pymol.
import filename_to_script  (without .py)
If the script filename is "forster.py)", you write
import forster

Then you have access to the functions which have cmd.extend("forster",forster)

cd /homes/YOU/Documents/Atto-dyes/Spectre/ALEXA488-ALEXA633
import forster
forster D_Exi=ALEXA488Exi.txt, D_Emi=ALEXA488Emi.txt, A_Exi=ALEXA633Exi.txt, A_Emi=ALEXA633Emi.txt, A_e_Max_Y=159000, A_e_Max_X=621, Qd=0.92
And you have access to other functions with name of file in front of function
Area=forster.numintegrator(fluarray, col1=0, col2=1)

Best
Troels



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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 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



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