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 '
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 e
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
