On 4/28/14, 7:53 AM, meginir urestal wrote: > how does modeller handle alternate sidechain positions in a pdb file?

From http://salilab.org/modeller/9.13/manual/node175.html

"For PDB files with alternate locations (characters in column 17 of ATOM or HETATM records), MODELLER reads only the first alternate location encountered for each residue."

Ben Webb, Modeller Caretaker