update: multi-resolution docking with Situs 1.3

Willy Wriggers wriggers at scripps.edu
Thu May 18 14:54:55 PDT 2000

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

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

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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