You are correct that PyMOL cannot properly handle structures which do not have unique names within a given residue. The "rename" command will make sure all atoms are unique identified:
fragment arg, myobj
From: Sébastien Conilleau [mailto:sconilleau@...]
Sent: Tuesday, January 06, 2009 5:00 AM
Subject: [PyMOL] Updating modifications
I try to write a script able to reorient a protein and to save (in a pdb format) the reoriented structure.
I have a problem during the saving phase of my script.
When I use the update function some atoms are not tacken into account. Typically, if several atoms have the same name (for example HB of a sidechain) only the first one is updated. This leads to a final wrote structure with a series of atoms badly positionned.
Do you have any idea to solve this problem ?
Thank you for your help