[phenixbb] revisiting "Problem with loop fitting "
alebus at pasteur.edu.uy
Sun Feb 23 10:11:49 PST 2014
it worked! thanks a lot
I followed your suggestions first with one loop (I have six monomers in
the ASU, so I have say 12-18 loops I would like to build in): the
program chose the best fit with CC of 0.54. ...and a couple of
Ramachandran outliers appear now in this added loop as well.
So, I would like to ask for your advise here, if I may; just a very
brief explanation of the specific problem:
this is a case where the density clearly says a loop should be built in,
but simultaneously, is not at all a "good density" (this is why the
loops are actually missing, at this, rather advanced, point of the
Let me just add that resolution is 2.75A, but I have 0.42 hemihedral
twinning in P65 (twin law k,h,-l)...best crystal and data we could get
after lots of work: so, maps are good, but definitely not great.
If I attempt adding these loops manually, it is not easy...and typically
end up having too many Ramachandran outliers (and don't want to add
phi/psi restraints in refinement)
I would so much appreciate any hint, as to the best way to handle this
kind of situation to automatically build at least stereochemically
correct loops, in clear but not easily interpretable electron density.
Many thanks again Tom for your help
On 2/23/14, 12:39, Terwilliger, Thomas C wrote:
> 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
Alejandro Buschiazzo, PhD
Unit of Protein Crystallography
Institut Pasteur de Montevideo
Phone: +598 25220910 int. 120
Fax: +598 25224185
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