[phenixbb] revisiting "Problem with loop fitting "

[Terwilliger, Thomas C]

Hi Alejandro,

I think that the documentation is not clear enough about how to specify the gap (I will fix this).  Try this test:

   phenix_regression.wizards.test_command_line_loops test_fit_loops

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,
Tom T


________________________________________
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






--
Alejandro Buschiazzo, PhD
Research Scientist
Unit of Protein Crystallography
Institut Pasteur de Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY
Phone: +598 25220910 int. 120
Fax:   +598 25224185
http://www.pasteur.edu.uy/pxf

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