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) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabotti@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm

"If you think you are too small to make a difference, try sleeping with a mosquito"