Hi Alejandro, I think that the documentation is not clear enough about how to specify the gap (I will fix this). Try this test: phenix_regression.wizards.test_command_line_loops test_fit_loops Then modify the command in that test: phenix.fit_loops pdb_in=nsf_gap.pdb mtz_in=resolve_0.mtz seq_file=nsf.seq start=37 end=43 chain_id=None to match your PDB file and mtz file. The confusing thing (I think) is that start=37 means the first residue in the gap is 37, not the last residue already present is 37. Let me know if that doesn't do it! All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Alejandro Buschiazzo [[email protected]] Sent: Saturday, February 22, 2014 2:28 PM To: [email protected] Subject: [phenixbb] revisiting "Problem with loop fitting " Dear phenix community I am attempting to use phenix.fit_loops for the first time and getting an error message: "No suitable gap found matching residues" I found a short exchange exactly about this (Jan 2011), but eventually Tom Terwilliger asked for the files directly to see if he could solve it. I can't seem to find a later summary of the solution. (apparently, the most probable reason was some kind of mismatch between PDB numbering and sequence file...which I shouldn't have... I'm probably missing some silly here - I have been fiddling around with the sequence file in many ways...with no success) many thanks for any help! alejandro -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb