Subject: Re: [modeller_usage] occupancy <1 in my models
From: Modeller Caretaker <>
Date: Tue, 25 May 2010 09:50:16 -0700
Cc:
On 5/25/10 2:05 AM, Anna Marabotti wrote:
I obtained a model of a protein using Modeller 9v7. Looking at the resulting
PDB file, I saw that several atoms (in some cases the entire sidechain, in
other cases only one or two atoms) show an occupancy<1 (typically 0,5, but
also 0.3 in some cases).
For residues aligned with a template, the atom occupancies will simply
match whatever was in the template file.
In the template, the corresponding residues show
two or sometimes three alternative conformations of their sidechains, with
occupancy<1, so I imagine that Modeller chose one of the conformations and
transferred directly the information about occupancy in the PDB file it
creates. My question is: what is the criterium that Modeller follows to
choose one alternative conformation? It simply chooses the first one, or are
there other criteria?
And what about the fact that a single atom has an
occupancy<1 without any other alternative conformations? Could this be able
to perturb the protein behavior?
Modeller does not use the occupancy information in the model, so this
won't affect the generated models.