You can specify a residue by it's sequence number and chain ID rather than it's name. So if your single-residue molecule is open as model 0 and your snapshot structure in model 1, and you wanted to match the single residue with residue 31 in chain A of model 1, this would do it:

Eric Pettersen

UCSF Computer Graphics Lab

On Feb 4, 2008, at 6:59 AM, Francesco Pietra wrote:

Task: compare/align a single-residue molecule before docking (naked molecule,
mol2 or pdb file) with same residue as ligand in a protein after docking/MD
(pdb file of a snapshot for complex embedded in a bilayer membrane). Should I
change the residue name in one of the two models? Same name poses to me
problems. Or there is a direct way?
Thanks
francesco pietra

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