[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
> LABIN LINE: FP=2FOFCWT PHIB=PH2FOFCWT
>
>
> 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
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
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