[phenixbb] Can Phenix do MR with medium/low res EM models?

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Mar 19 12:44:28 PDT 2009

Hi Gino,

I have never tried any problem of this size...but here is a way to proceed
using Randy's "input_partpdb_file" option for Phaser that is now available
in the autosol wizard.

Take your EM model with all its NCS copies, and give it to AutoSol with
the keywords:

partpdb_rms= 3.0

The partpdb_rms should be the estimated RMSD between the MR model and the
true model. You will have as good an idea about this as anyone...

You also would supply the usual information to autosol:

phenix.autosol sad-data.sca seq.dat 450 Se f_prime=-8 f_double_prime=4.5 \
    build=False input_partpdb_file=MR.pdb\
    partpdb_rms=3.0 \

You might cut the resolution to a pretty low value like 6 A as above.

If you get a lot of good sites refined by phaser, then you may be on the
right track. This autosol run will output phaser_1.mtz and also
resolve_1.mtz that you can use as a starting point for further density
modification and model-building as appropriate.

Given the size of this problem, I would anticipate lots of challenges, and
we will be happy to help as you carry on with it.  You might try running
everything at really low resolution (20A) at first just to get things to

All the best,
Tom T

Hi Phenix community,

I was wondering if Phenix can handle MR starting from medium/low res EM
I have a very large oligomeric protein (2.4MDa) with lots of NCS and >450
In principle, I could use low res MR phases from the "replaced" model to
locate Se-sites and
then NCS-averaging to locate more sites and improve my phases.

Any suggestions how to get Phenix to use an EM model?
Has anybody done it successfully using Phenix?

Thanks in advance,


Gino Cingolani, Ph.D.
Assistant Professor
Dept. of Biochemistry and Molecular Biology
SUNY Upstate Medical University
750 E. Adams Street, Syracuse, NY, 13210
Tel.   (315) 464 8744
Fax.  (315) 464 8750
Email:  cingolag at upstate.edu
"Nati non foste per viver come bruti,  ma per seguir virtute e conoscenza"
("You were not born to live like brutes, but to follow virtue and
Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120)
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