Re: [ccp4bb]: Self rotation on electron density map

[R J Read <rjr27@cus.cam.ac.uk>]

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On Mon, 17 Jul 2000, Sheryl Tsai wrote:
> 
>     I need to do self-rotation on electron density maps in order to find a
> non-crystallographic 2-fold.  Is there any software that can do so?  Thank
> you very much for your help!
> 
This is what we had to do as part of solving the structure of pertussis
toxin.  The NCS 2-fold couldn't be found with a self-rotation function (I
presume you have the same problem), but the Wang envelope gave a
reasonable indication of where the two molecules were located.  We cut out
spheres of density corresponding to each of the two molecules,
back-transformed to get structure factors, and used those two sets of
structure factors in a cross-rotation function, which gave a clear peak.
Then one of the spheres of density could be rotated, back-transformed and
used in a phased translation function to find the translation part of the
NCS 2-fold operator.  The methods to do this are described reasonably well
in a review article that Gerard Kleywegt and I wrote (Structure 5:
1557-1569, 1997).

We did this with a combination of purpose-written programs and the DEMON
package of Fred Vellieux.  But since then the most convenient software
I've discovered for the operation of cutting out density is the program
GHKL written by Liang Tong. This will do the equivalent, in reciprocal
space, of computing a map, cutting out a sphere of density, rotating it,
placing it into an arbitrary unit cell and even applying symmetry, then
back-transforming it to give new structure factors.  At that point you can
use your favourite molecular replacement program, such as AMoRe.

I haven't tried to do anything similar within CCP4, but it could probably
be done: create a large spherical mask, apply that to your map and then
invert the map.  Perhaps others could comment on how to do this
efficiently within CCP4 or RAVE?

Randy J. Read
Department of Haematology, University of Cambridge
Wellcome Trust Centre for Molecular Mechanisms in Disease
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building     Tel: + 44 1223 336500
Hills Road                      Fax: + 44 1223 336827
Cambridge CB2 2XY, U.K.         E-mail: rjr27@cam.ac.uk