Hi,
to get the angle between 4 atoms, use get_dihedral. For angle between 3 atoms
(lines intersect) use get_angle.
http://pymolwiki.org/index.php/Get_Angle
http://pymolwiki.org/index.php/Get_Dihedral
Cheers,
Thomas
PS: it's nice to give your name in an email to a list like this one
On 12 De
Hi all,
I'm trying to write a script to data mine the pdb. I'm want to look at the
ligands in a pdb file and fish out those that meet a certain criteria. I've
got a script that can look at the ligands all at once but I need to assess
each ligand individually. Since I'm looking at 40,000+ pdbs I ne
Katherine,
not sure if that is what you are looking for but you can select for non-polymer
residues with:
select lig, prot and organic
That will select any non polymer (protein and R(D)NA) residues present in the
pdb. You then would need to break the selection further into the individual
cons
Hi Carsten,
Thanks for the help. I've tried variants of that selection and it works
great if there is only one ligand. Unfortunately it breaks down when there
are multiple ligands and they don't all fit the criteria. I'm surveying
almost half the PDB so these are all different proteins with differ
Hi Katherine,
PyMOL can do what you want. I've done this exact task before.
Here's the idea. If you have a PDB with multiple ligands and you use,
select allLigands, organic and myProtein
you create the selection allLigands which contains all the ligand
atoms in myProtein. What you need to do
