[phenixbb] Phaser, Phenix and Em models

Gino Cingolani cingolag at upstate.edu
Fri May 8 07:39:17 PDT 2009

Hi Randy,

what about implementing the use of EM-models (e.g. structure factors
from EM model) in Phenix to carry out MR and/or MR-SAD?
There's a growing number of macromolecular complexes that have been imaged
at medium/low res by EM, which could be of great help to
phase at low res or located anomalous scatterers in phased maps.
And the EM database keeps growing!

At this moment, it is certainly possible to use EM models in Phaser, 
but the Phenix pipeline could add much more to that. For instance, 
Phenix would allow for better phase extension of low res EM phases to higher
res by ncs-averaging or multi-crystal averaging (in Resolve). 
Or Phenix could help combining low res EM phases with other phase 
sources such as SeMet sites, poorly occupied heavy atom sites, etc (MR-SAD).
Or Phenix could rigid body refine (at low resolution) pseudo-atomic models
obtained by filling in EM-models with dummy atoms. 
This would help defining averaging masks and so on.
What do you think?

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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