[phenixbb] mr_rosetta question

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Fri Jul 17 19:18:29 PDT 2020

Hi Wei,

Your sequence file should be 1 copy of the unique sequence.

Your search model should be either your original search model, or probably
better, any one copy of a placed and already refined model (just take your
A chain from your existing solution and call it a search model).

Your fixed_model consists of the 5 placed copies you already have.

Your value of ncs_copies is 1 if you are using a fixed_model to hold the 5
existing copies.

This approach assumes that the 6th copy is not that similar to the other 5
and NCS averaging will not be useful. Note that there is an alternative
approach to do all this that involves specifying the translations and Euler
angles of the 5 placed copies.  This alternative method will apply NCS to
all 6 copies and will work much better than the way described above if all
copies actually are very similar.  Probably the way described here is
better for your case because you get the advantage of using the refined
positions of the first 5 copies to get an accurate description of most of
the cell contents and as mentioned below the 6th copy ma not be similar.

Note also that the chances of success are low because you already tried to
find the 6th copy with Phaser and it didn't work.  MR-rosetta could
possibly work if the 6th copy is just in a different conformation.  If it
is disordered or otherwise not visible...it is not likely to work.

You might also just look very carefully in your 2mFo-DFc map for any
indication of where the 6th molecule may be located.  If you can see a hint
of it, a real-space search may be worth trying instead of further molecular
replacement.  Also extensive auto-building could possibly show you where
the 6th copy is located.

If you want to try the alternative approach, see here:

under this description:

fixed_ensemblesIf you already know the placement of one or more molecules
you can specify them as fixed ensembles. NOTE 1: you are specifying
location and orientation of one or more copies of the search model NOTE 2:
you cannot specify use_all_plausible_sg if you have fixed ensembles

fixed_ensembleID_list = NoneEnter the word 'ensemble_1' to indicate that
you want to specify a copy of your search model that is to be fixed. To
specify more than one placement just say 'ensemble_1' more than once. For
example if you


Let me know if that doesn't do it or if I gave you any of the parameters

All the best,
Tom T

On Fri, Jul 17, 2020 at 7:07 PM Wei Wang <ww2283 at columbia.edu> wrote:

> Dear all,
> I would like to get help on a mr_rosetta run. I have a case that 5 copies
> of searching model was found by Phaser, and I would like to find the sixth
> one. In addition I would like to improve the building of the MR solution.
> In such case I’m considering a mr_rosetta run, with some parameters like
> this: phenix.mr_rosetta seq_file=seq.dat search_models=placed_5_copies.pdb
> already_placed=true ncs_copies=1 …
> My question is, should I use the already placed 5 copies model as
> search_models, with ncs_copies=1, or should I use the original searching
> model with ncs_copies=6 (in this case I guess I should get rid of the other
> four copies from the result of Phaser)? For seq.dat, should I use the
> sequence from one copy of searching model, or paste 5 copies into the
> seq.dat?
> Thanks,
> Wei
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Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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