[phenixbb] Phaser, Phenix and Em models

Maier Timm timm at mol.biol.ethz.ch
Mon May 11 10:17:20 PDT 2009

Hi Gino, Tom and Randy, 


I would rather argue for a future  "specialized" phenix low res
molecular replacement application/wizard  than for simple conversion to
throw an EM map into a standard MR procedure. In my experience, MR with
EM models is significantly more complex than with a molecular model for
several reasons. For example, 


-          the EM maps may suffer from scaling errors which can have a
severe impact on packing function scores  and downstream averaging
procedures, so an automatic "scale grid search" would be really useful. 

-          EM maps sometimes are affected by accumulation of density
along axes of symmetry of particles  which can severely bias the
outcome. Sometimes grid searches for the origin of symmetry combined
with initial low-res averaging steps are helpful. 

-          Maps without an associated molecular model are difficult to
break into conformationally rigid parts. Although many EM structures are
derived on the basis of conformational classification or sorting, this
information is not usually presented in a useful way in publications or
database depositions. 

-          Negative stain (cryo) EM maps are particular prone to
conformation distortions due to staining artifacts.

-          For particles with strongly preferred orientations on the EM
grid, the maps may have some special features 

-          ...


A preferred application for (low-res) MR from EM maps ( or also SAXS
data ???)  would ideally be able to solve some of these problems. A
plain density to structure factor conversion as an entry to standard MR
can already easily be done manually.  But if it's done automatically
without overcoming the above problems, many research will once try
"automated MR from EM" through wizard X. If this ends unsuccessfully,
they may believe their problem could simply not be solved and feel
discouraged from investing a little more time and finally miss a chance
to solve their problems. 







Dr. Timm Maier

ETH Zurich

Institute of Molecular Biology and Biophysics

HPK H 5 

Schafmattstr. 20

8093 Zurich


e-mail: timm.maier at mol.biol.ethz.ch

phone ++41 44 633 3148




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