Re: [PyMOL] Analysis of docking poses from 2 nmr-ensembles

[Sampson, J. M. <jm...@cu...>]

Hi James -

First, it will be useful to split the states<http://www.pymolwiki.org/index.php/Split_states>.

split_states ensemble1
split_states ensemble2
delete ensemble1
delete ensemble2

Then, superimpose<http://pymolwiki.org/index.php/Super> all structures onto a reference structure for easier visualization.  This won't affect your distance measurements, but will make it easier to see the changes from one object to the next.

python
ref = 'ensemble1_0001'   # your reference object
for obj in cmd.get_names():
    if obj != ref:
        cmd.super(obj, ref)
python end

For your residue pair analysis, you have to decide what kind of distance you want to measure (e.g. CA-CA; average position of all atoms in the residue; closest atoms, which would require looping through all atom pairs in each residue pair and keeping only the shortest distance).  Then create selection strings based on those criteria, use them in distance<http://pymolwiki.org/index.php/Get_Distance> measurement, and print them or add them to a variable to be output.  If you want to create and visualize distance objects, use `distance` instead of `get_distance` and pass a distance object name as the first parameter before the selections.

python
sel1 = "resi 100 and name CA"
sel2 = "resi 200 and name CA"
sel3 = "resi 300 and name CA"
for obj in cmd.get_names():
    d12 = cmd.get_distance("{} and {}".format(obj, sel1), "{} and {}".format(obj, sel2))
    d23 = cmd.get_distance("{} and {}".format(obj, sel2), "{} and {}".format(obj, sel3))
    print "{}: '{}' to '{}' distance = {}".format(obj, sel1, sel2, d12)
    print "{}: '{}' to '{}' distance = {}".format(obj, sel2, sel3, d23)
python end

This is just a very quick example; really there are many different ways to do this, and you'll have to find what kind of analysis your particular structure needs.  Also, if you want to look at H-bonds, it will be more complicated, because the angle is important as well.  In this case you may want to look at Thomas' Polarpairs<http://pymolwiki.org/index.php/Polarpairs> script.

Hope that helps.

Cheers,
Jared



On Jun 13, 2016, at 9:41 AM, James Starlight <jms...@gm...<mailto:jms...@gm...>> wrote:

Dear Pymol users!

I am studying protein-protein assosiation using 2 different proteins
as test case by means of variety of computational methods.
For my particular caseI need to compare binding poses emerged as the
result of protein-protein docking (ensemble 1: which  consists of 20
snapshots according to docking ranking) as well as MD simulation
(ensemble 2: which consists of 10 snapshots each of which represents
binding pose which has been established during long MD run).
Loading those two ensembles in pymol as 2 different models (in
NMR-like model format)  I need to performs some analysis  to find some
shared trends in each of them e.g RMSD of the distances between common
residues-pairs found in contact map analysis
or something else. What are most trivial suggestions might be in that
particular case?


Thanks for the suggestions!


James

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