Dear All,
I have a small query regarding PyMol and I would appreciate if you can help me
with it. My query is:
How do I analyze interactions with PyMol after I have docked my files? I wanted
to know which molecules/amino acids are interacting in the docked confirmation.
I would really
Hello especially for those who are experienced using Contact Map Visualizer
Plugin. About generating a contact map, after typing the following command as
shown:
g_mdmat -f 2p31.pdb -s 2p31.pdb -mean contact-map.xpm
It gives us a list of group selection to analyze such as below: Select
Hi Suheila,
The CMV requires the contact map and the structure to match. So to get
what you want, it's easiest to load the structure in pymol, and save
only the part you want to analyze:
save helix.pdb, ss h
save sheet.pdb, ss s
Then you can run g_mdmat on each of those, and load the result
OK. I can see a bit clearer now :) Yet which leads me to another question.
About the group selection analysis below: Select group for analysis
Group 0 ( System) has 2616 elements
Group 1 ( Protein) has 2470 elements
Group 2 ( Protein-H) has 2470 elements
Group 3 ( C-alpha) has 314 elements
Hi Hani,
with PyMOL you can visualize polar contacts, using the distance
command with mode=2 argument. See the PyMOLWiki page:
http://pymolwiki.org/index.php/Distance
Example:
distance interface, chain A, chain B, mode=2
However, this is not really a analysis of the interface. Instead I would
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I see!
Many thanks
Tsjerk! XD
Date: Mon, 19 Mar 2012 20:59:08 +0100
Subject: Re: [PyMOL] Query on 'Select group for analysis' for Contact Map
Visualizer Plugin
From: tsje...@gmail.com
To: bell_beaut...@hotmail.com
Hi Suheila,
These groups are for selecting specific subgroups of a
