A similar question: Does PyMOL have a PDB file parser that can read
disulphide linkages from the file and connect the atoms or one has to
explicitly issue bond commands. Also, can PyMOL display hydrogen bonds
without the user having to write out a list?
thanks,
Kaushik Raha.
Penn State
Hello fellow PyMOL users,
I am trying to display a ccp4 map over just a ligand. I have
successfully read in the map and displayed it around the ligand with:
isomesh msh1, map1, 1.5, myobject
but the map has bits and peices of the surrounding sidechains.
Is there a way to only display the map
Scott,
isomesh msh1, map1, 1.5, myobject, carve=2.1
The postfix carve=2.1 will trim density which is more than 2.1 A from
myobject.
You may want to play around with the exact cutoff...
Cheers,
Warren
-Original Message-
From: Scott Classen [mailto:clas...@uclink.berkeley.edu]
On Fri, 20 Sep 2002, Kaushik Raha wrote:
Warren,
Thanks for the h-bond tip. A related question, I was wondering if PyMOL
can protonate ligands on its own. In other words can it perceive the
atom-type. I have been trying to integrate a perception algorithm
If your ligands come in with
