Uppsala Software News @ 960801
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* ESSENS Version 1.1
********
New scoring function implemented, following a suggestion of Morten
Kjeldgaard.  Scoring function option M = Morten's variant of the
K-minimum sum function.  The actual function is the same, but instead
of assigning the score only to the pivot point, it gets assigned to
*all* grid points near atoms in the template.  This means that if a
fragment fits well, an entire image of it is "imprinted" in the score
map, which upon contouring will not only show where the template
fitted the map, but also *how* it fitted (i.e., in which orientation).
Initial experiments show that you really get nice strands and helices
in which even the CB atoms can be discerned (making it easy to see the
directionality of alpha helices due to their typical "Christmas-tree"
shape, with the sidechains pointing "down" toward the N-terminus).
  Using Morten's method, hepta-Alanine templates, 20-degree steps for
the rotational search and a density cut-off of zero, we can now detect
our helices and strands in something like 1 to 2 CPU hours on a
moderately fast Alpha (for P2 myelin; for glyoxalase ~3-5 hours each) !
Also, you don't need to apply any cosmetic map filters afterwards.
  If you look for helices and strands and use scoring option "M"
(version 1.1 and higher), we now recommend the following set of input:
   - map - your best experimental map; grid spacing ~1 A (1/3 of the
     high-resolution limit)
   - mask - helps speed up things, so use one
   - templates - 5 or 7 residue oligo-Ala in alpha or beta conformation
   - Euler angle search in 20 degree steps
   - scoring method "M", with about 60% of the atoms used to compute
     the K-minimum sum function (i.e., 15 atoms for penta-Ala, or
     21 for hepta-Ala)
   - density cut-off of 0.0 provided the average density in your
     (unit cell) map is zero
  The manual has been expanded with lots of advice and hints w.r.t.
parameter and template choices.  You can always check the latest
version of the manual via the home page of the Uppsala Software
Factory at URL:
    http://onyx.bmc.uu.se/~gerard/manuals/gerard_manuals.html
This document also contains new, cut-and-pastable templates (e.g.,
hepta-Ala in alpha and beta conformation).
  I will try to set up a little demo at the Seattle meeting (at the
DEC booth).


* DATAMAN Version 4.1.2
*********
Bug fixed in RFree COmplete command (which creates N reflection
files for use in complete cross-validation exercises); it
occured when writing these files.


* LSQMAN Version 4.7
********
Long-standing bug in the EXplicit command fixed (sometimes popped
up when all (non-H) atoms were compared and the atoms in the two
molecules were not in the same order - very sloppy !).  Please,
get the new version from the server if you use this program.
  New FIx_atom_names command to reduce artificial differences
(in all-atom RMSDs and side-chain torsion-difference plots) due
to chemically indistinguishable atoms being swapped in two
molecules (e.g., two Phe rings related by a 180-degree "flip"
will have an RMSD of ~1.5 A and a CHI2 differing by ~180 degrees,
even though the two conformations are identical).  Check the
manual for more details on how and when to use this command.


* FAQ
*****
Both the FAQ itself, and the script to convert it into HTML
(Morten's "rfaq") have been reworked and updated.  The WWW
version of the FAQ now contains many hyperlinks to manuals
(O-related programs, CCP4 programs, X-PLOR, etc.) and other
material.  Check it out at URL:
    http://kaktus.kemi.aau.dk/ofaq/ofaq.html


--cd