Hi Sri,
if you have your structure loaded into PyMOL, you can make named
selections for your peptide sequences like this:
select pep1, pepseq RMFLS
select pep2, pepseq KGHGK
select pep3, pepseq ALSDL
There are also scripts available for pattern matching, for example:
http://pymolwiki.org/index.php/FindSeq
Highlighting the selections with colors:
color white
color red, pep1
color blue, pep2
color green, pep3
You can query these selections on various properties:
# (approximate) surface area
set dot_solvent
get_area pep1
# secondary structure
print [a.ss for a in cmd.get_model('pep1 and name CA').atom]
Doing this on a large number of structures is possible if you write a
python script, which requires general programming skills. All the
commands shown above are accessible from the PyMOL python API. Examples:
from pymol import cmd
cmd.select('pep1', 'pepseq RMFLS')
cmd.color('red', 'pep1')
print cmd.get_area('pep1')
Hope that helps.
Cheers,
Thomas
Sri Ramarathinam wrote, On 11/22/12 08:16:
> Hi All
> I am very new to using Pymol. I am wondering if anyone can point me towards the right direction with the following:
> 1) I have a list of peptides and would like to know what their location is on their respective proteins which already have structures in PDB (surface exposed, buried, helix, loop or beta sheet?)
> I guess I could do it manually but the peptide list could go into hundreds and would be nice to see if there a command line or a script I could use.
> 2) Can i ask Pymol to show the peptide's location on the 3d structure of the protein? perhaps in a different colour to highlight location?
> Manually I would select on the sequence and show as whatever I want but is there a command to automate a huge list?
>
> Is it possible to do these tasks with Pymol or is there any other software I could be using?
>
> Thanks very much for your help,
> Cheers
> Sri
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
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