Dear PyMol users!
Some of docking servers (e.g swiss dock) which I'm using need in
explicit definition of the coordinates (in XYZ) of the docking region
as well as coordinates of its COM. How I could obtain such coordinates
of intrested pdb file based on the knowing protein-ligand interaction
I'm thinking a good work around is simply this.
Select the binding site of the amino acids and ligand in pymol.
Then copy those selected aa's and atoms to another object:
save - model - copied_object as output.pdb
output.pdb will then contain all the x,y,z coordinates of only what was
Jordan,
Thank you for advise.
I've tried to do the same already but
1- In Resulted pbd file ( with ligand and surrounded residues only)
the coordinates of ligand and residues have been changed in
comparison to the initial pdb/ How to prevent it?
2- The resulted pdb consist of coordinates of
Hi James,
the get_extent command in PyMOL will give you the corners of the
selected region, from which you easily can calculate center and edge
lengths.
http://pymolwiki.org/index.php/Get_extent
Example:
box = cmd.get_extent('sele')
print 'Center:', [(a+b)/2.0 for (a,b) in zip(*box)]
print
Dear all!
I have input multi state structure consisted of protein in one state
and ligand in the second state generated by Chimera. I want to merge
both of that objects in one common object. How I could do it?
James
2012/7/18 James Starlight jmsstarli...@gmail.com:
Dear all!
I have input
