[phenixbb] Problem with loop fitting

Tom Terwilliger terwilliger at lanl.gov
Mon Jan 24 13:31:46 PST 2011

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
> No suitable gap found matching residues  331 - 336  chain:  A
> No final model obtained
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
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