[phenixbb] Problem with loop fitting

Kendall Nettles knettles at scripps.edu
Mon Jan 24 13:41:18 PST 2011

The gap is there, but I'm not sure if I have generated the sequence file correctly. I used a fasta format of all the amino acids in the protein construct. The first three are from the tag, and then the sequence starts at amino acid number 299. The amino acid that is first visible varies from structure to structure and between chains in the same structure, and is between 299 and 307. For the structure I tried the loop fitting it starts at 305. Should I trim the beginning of the seq file? Do I need to tailor this file for each structure I run it on?


On 1/24/11 4:31 PM, "Tom Terwilliger" <terwilliger at lanl.gov> wrote:

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
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Los Alamos National Laboratory
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