update: multi-resolution docking with Situs 1.3

[Willy Wriggers]

Hi all,

Subsequently to the last announcement on this list, two new versions of
the free single-molecule, multi-resolution docking package went online
at URL http://www.scripps.edu/mb/wriggers/situs - the current version is
1.3.

I would like to ask all folks who downloaded the software but have not
registered to please send me a note - registration is voluntary but
helps us to justify the "fundingworthiness" of Situs in upcoming grant
proposals.

FYI: Some of the new functionalities are appended to this mail. More
info can be found online.

Best wishes,
-- 
Willy Wriggers, Ph.D.
Department of Molecular Biology, TPC6
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, California 92037
E-mail: wriggers at scripps.edu
URL: http://www.scripps.edu/mb/wriggers
Tel: (858)784-8823
Fax: (858)784-8688


--
New features of Situs 1.3 relative to version 1.1:
--------------------------------------------------

1. The rotational and positional precision of a fit are estimated based
on statistical variability measures.

2. A web tutorial has been added for the *flexible* fitting of
high-resolution structures to low-resolution density maps using Situs
and X-PLOR.

3. A new tool, pdblur, has been added for lowering the resolution of
atomic structures. pdblur performs a real-space convolution of atomic
structures with template density kernels ("point-spread functions").
This blurring of data is useful e.g. for creating simulated EM density
maps from atomic structures.

4. Skewed (non-orthogonal) unit cells in EM maps are automatically
converted to cubic lattices (required for Situs), using tri-linear
interpolation. The convert program now reads and writes ASCII, X-PLOR,
MRC, SPIDER, and CCP4, EM map formats.

5. Situs 1.3 has been ported to SGI, PC/Linux, Sun, and Hewlett-Packard
architectures (GNU gcc compliant). 

6. A new user-friendly vector-quantization and docking routine, "qrange"
consolidates the older routines, qdock, qvol, into a single utility.
qrange evaluates fits automatically for a range of number of vectors.
The user can select the optimum number of vectors and the resulting fits
based on objective criteria.
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