Atomic model building by docking.
roseman at mrc-lmb.cam.ac.uk
roseman at mrc-lmb.cam.ac.uk
Fri Dec 6 02:06:13 PST 2002
Dear 3D EM list members and colleagues,
I am pleased to announce a new - much faster - release of DockEM, my
program for building atomic models of macromolecular complexes by
fitting/docking the structures of domains into EM density maps.
Extensive searches of complete volumes can now be done in under 24 hours on
a (single) standard workstation. These are complete exhaustive 6 parameter
searches of the rigid body models of domains in the entire volume of the
map of the macromolecular complex.
For example; for a 12 A map of GroEL (or the GroEL-GroES complex)
sampled at 4 A/pixel the full search of the 64 cube map will take ~18 hours
on a DEC alpha workstation with a 600 MHz EV6 processor. That is sampling the
angular space in 4 degree intervals. A finer angular search of 2 degrees
that is restricted to a 32 cubed region (about 3 asymmetric units) will
take ~15 hours.
The program is still essentially as described in the original publication
(Roseman 2000, Acta Cryst D56, 1332-1340.), but the new version takes
advantage of a Fourier algorithm for implementing the real-space
correlation, that I have recently developed. For details see my
Ultramicroscopy manuscript, in press, available online 29 October 2002.
This manuscript describes a 2D application of the fast local real-space
correlation function for particle picking from electron micrographs. See
articles in press, Ultramicroscopy, science direct,
(http://www.sciencedirect.com)
Please contact me if you would like an update or you would like to use the
program.
Yours sincerely,
Alan Roseman.
-----------------------------------
Research Associate
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
England
CB2 2QH
roseman at mrc-lmb.cam.ac.uk
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