[PyMOL] Problem with finding polar contacts

Hi,
I ran into a bug with the find polar contacts function (distance with 
mode=2) today. The problem arises when I was trying to find the hydrogen 
bonds between a ligand and a receptor that had been processed with 
reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A 
bug/feature of reduce is that when it adds hydrogens, it gives all of 
the newly added hydrogens a 0 as the atom index in the pdb file.
So what happens is when you try to find the polar contacts between the 
ligand and the receptor, it draws a bond between a ligand atom and the 
last hydrogen (which happens to be non-polar) which is 12 A away. I'm 
guessing it is because pymol is using the atom index from the pdb.
One possible alternative would be to index based on the set of the atom 
id, atom name, residue name, chain id, and residue ID, but I don't know 
how feasible that is.

The work around that I have found is to pass the receptor through babel 
after processing with reduce. babel prot.pdb prot2.pdb , which 
re-indexes the atom ids.

Matt Baumgartner

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