[phenixbb] autobuilding homomers

Terwilliger, Thomas C terwilliger at lanl.gov
Sun Oct 28 07:40:33 PDT 2012

Hi Ingemar,

This is an interesting case.  It is a little difficult to tell exactly why your model does not end up with 3 more-or-less identical monomers.  The basic question will be: "Is there really near-perfect NCS in the structure?".  Here are some things to try:

1. Take your best model and run phenix.find_ncs with that model to get an NCS parameters file (find_ncs.ncs_spec).  Check that this file does have 3 NCS copies.

2. Try applying the ncs from find_ncs.ncs_spec to your "best" monomer to generate a trimer:

  phenix.apply_ncs my_best_monomer.pdb find_ncs.ncs_spec

Now look at this "perfect" trimer.  Do the 2 generated monomers actually match up with parts of the original model?  Or instead, is the NCS not really so perfect?

3. Try running autobuild starting from your "perfect" trimer, with rebuild_in_place=False (or also try with rebuild_in_place=True).

4. Take your best map from your best working model, throw away the model, and run autobuild starting from the map with input_map_file=my_best_map.mtz and let it build everything from scratch.

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Ingemar Andre [ingemar.andre at biochemistry.lu.se]
Sent: Sunday, October 28, 2012 6:35 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] autobuilding homomers

I have a question about the proper procedure for building homomers. My
test case is a trimeric coiled-coil with 3-fold symmetry (trimer in
assymetric unit). My input model is a trimer with three chains (A,B,C)
with identical sequence. If I run phenix autobuild
(rebuild_in_place=False) with this model I get a structure with decent
R/Rfree. However, there are some issues:

1) Helix 1 consists of chain A in the output structure. There is a
jump in the sequence number for chain A at the end. However,
disregarding this chain break the full sequence is correct for helix 1.
2) Helix 2 consists of chain B + C in the output structure. The chain
B has the correct sequence for helix 2. Chain C has partly the right
sequence for helix 2.
3) Helix 3 consists of chain C in the output structure. Chain C has
partly the correct sequence for helix 3. Lots jumps in the sequence

GIven that I know its has three subunits with identical sequences I
gather it should be possible to have autobuild generate structures
with three chains with identical sequences. I have tested a few
things. With and without giving it the sequence file corresponding to
the sequence of a monomer. With and without enforcing ncs based on the
input model (find_ncs=False input_ncs_file=find_ncs.ncs_spec). I am
never able to build sequence-symmetric structures with
rebuild_in_place=False for any homomer I have tried to build. I have
limited experience with phenix so it is likely I am missing something
obvious. In any case, I would appreciate your input on this.

Best regards,


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