Hi Kendall, Oh I see. No, you should be able to use the same sequence file for any model that has any (reasonable) set of fragments from that sequence. Might it be possible to send me directly ([email protected]) the input files and I'll give it a try here? All the best, Tom T On Jan 24, 2011, at 2:41 PM, Kendall Nettles wrote:

Tom, 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?

Kendall

On 1/24/11 4:31 PM, "Tom Terwilliger" 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 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: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss