Hi Kendall, Usually that would mean that there is no segment in your model that has a gap in chain A missing residues 331-336 (6-residue gap). It could also mean that the sequence could not be aligned with your sequence file. Is one of those possible? -Tom T On Jan 24, 2011, at 1:47 PM, Kendall Nettles wrote:
Dear PHENIX developers, I am trying fit_loops for the first time and getting error message: “No suitable gap found matching residues”
I’m not sure what the problem is.
Best regards, Kendall Nettles
knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A
# fit_loops # # Fit loops in a PDB file with gaps
# Type phenix.doc for help
Input sequence file is seq.dat Reading sequence from seq.dat Fit_loops: Fit a missing loop in a model. Map from: TEMP_cycle_best_refine_map_coeffs_1.mtz using labin FP=2FOFCWT PHIB=PH2FOFCWT Model from: Liganded_overall_best-coot-1.pdb LABIN LINE: FP=2FOFCWT PHIB=PH2FOFCWT
No suitable gap found matching residues 331 - 336 chain: A No final model obtained
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