[phenixbb] revisiting "Problem with loop fitting "

Terwilliger, Thomas C terwilliger at lanl.gov
Sun Feb 23 06:39:57 PST 2014

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 Buschiazzo, PhD
Research Scientist
Unit of Protein Crystallography
Institut Pasteur de Montevideo
Mataojo 2020
Montevideo 11400
Phone: +598 25220910 int. 120
Fax:   +598 25224185

phenixbb mailing list
phenixbb at phenix-online.org

More information about the phenixbb mailing list