[modeller_usage] occupancy <1 in my models

[Anna Marabotti <>]

Hi crew,
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). 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?

Many thanks and best regards
Anna

____________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
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Fax: +39 0825 781585
Email: 
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Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
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