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:


rename selection


For example:


fragment arg, myobj


alter myobj,name=’’


rename myobj






From: Sébastien Conilleau [mailto:sconilleau@chimie.u-strasbg.fr]
Sent: Tuesday, January 06, 2009 5:00 AM
To: pymol-users@lists.sourceforge.net
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

S. Conilleau