[phenixbb] revisiting "Problem with loop fitting "
Terwilliger, Thomas C
terwilliger at lanl.gov
Sun Feb 23 06:39:57 PST 2014
I think that the documentation is not clear enough about how to specify the gap (I will fix this). Try this test:
Then modify the command in that test:
phenix.fit_loops pdb_in=nsf_gap.pdb mtz_in=resolve_0.mtz seq_file=nsf.seq start=37 end=43 chain_id=None
to match your PDB file and mtz file.
The confusing thing (I think) is that start=37 means the first residue in the gap is 37, not the last residue already present is 37.
Let me know if that doesn't do it!
All the best,
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Alejandro Buschiazzo [alebus at pasteur.edu.uy]
Sent: Saturday, February 22, 2014 2:28 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] revisiting "Problem with loop fitting "
Dear phenix community
I am attempting to use phenix.fit_loops for the first time and getting
an error message:
"No suitable gap found matching residues"
I found a short exchange exactly about this (Jan 2011), but eventually
Tom Terwilliger asked for the files directly to see if he could solve it.
I can't seem to find a later summary of the solution.
(apparently, the most probable reason was some kind of mismatch between
PDB numbering and sequence file...which I shouldn't have... I'm probably
missing some silly here - I have been fiddling around with the sequence
file in many ways...with no success)
many thanks for any help!
Alejandro Buschiazzo, PhD
Unit of Protein Crystallography
Institut Pasteur de Montevideo
Phone: +598 25220910 int. 120
Fax: +598 25224185
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