[PyMOL] Peptide location mapping onto protein 3D structure

[Sri Ramarathinam]

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]

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

Post by Sri Ramarathinam
Hi All
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