Panagiotis L. Kastritis wrote: > Actually I understood what is going wrong... modeller renumbers > everything so at first it finds the residues of chain A that are > missing... However, the next ones will be 128-130 and not 1-3... > Is there a way to keep the initial numbering and not let modeller > renumber my structures? My last post should answer your question: http://salilab.org/archives/modeller_usage/2009/msg00245.html In this case you can't use option (1) because you won't have a PDB file containing the missing residues and their numbers (unless you manually create a dummy one; remember that Modeller only parses the ATOM/HETATM records, not SEQRES). (2) might be easiest if the numbering is sequential. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage