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 syssys.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-ALEXA633import 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
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2011/11/23 James Starlight <jmsstarli...@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 <jmsstarli...@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 <spel...@users.sourceforge.net>
>>
>>> Hi James,
>>>
>>> check this PyMOLWiki page:
>>> http://pymolwiki.org/index.**php/Fab<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://pymolwiki.org/index.php/CreateSecondaryStructure>
>>> http://pldserver1.biochem.**queensu.ca/~rlc/work/pymol/#**model<http://pldserver1.biochem.queensu.ca/%7Erlc/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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