Atomic model building by docking.

roseman at roseman at
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,

Please contact me if you would like an update or you would like to use the

Yours sincerely,

Alan Roseman.

Research Associate
MRC Laboratory of Molecular Biology
Hills Road
roseman at

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