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Yes, it's a nightmare. Sasha Urzhumtsev has written a Tcl/Tk-GUI based
Fortran program called CONVROT that allows you to convert any convention
of rotation angles or rotation matrices into any other, possibly
including crystallographic symmetry. This can be very useful if you want
to transfer informations between different program packages. But as
Eleanor said, the conventions within CCP4 should be consistent (the only
that I found in the past not to be consistent are the mask definitions
between SOLOMON and DM, but I haven't checked this in the last release
. . .).
Good luck,
Dirk.
Eleanor Dodson wrote:
I hate this problem - the only real guarantee you have it right is
when the correlation coeffs are reasonably high..
The CCP4/MR programs/LSQKAB/ DM etc conventions are consistent I believe
{R11 R12 R13 ] [XoA] [XoB]
[R21 R22 R33] [Y0A] = [YoB]
[R31 R32 R33] [Z0A] [ZoB]
Omat always prints/reads the transpose of that rotation matrix.
Transpose is the same as inverse, which means that if one matches B
to A rather than A to B you get the Omat which adds to the confusion..
Eleanor
Huiying Li wrote:
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I was running DM with 3-fold NCS averaging on a set of MR solutions
by PHASER. I have generated the NCS rotation matrix and translation
to bring molA to molB or molA to molC using either LSQMAN or
LSKAB(through CCP4i GUI 1.3.20 and ccp4-5.0.2). The NCS averaging
worked (final correlations are > 0.7 for NCS related molecules) only
if I used Euler angles to define the rotation/translation. When I
used the rotation matrix, either ROTA MATRIX or OMAT, the best
correlations were ~0.18 or ~0.4, respectively. I had the same
problems no matter running DM through CCP4i or with the script. It
seems DM has problems in interpreting the rotation matrix.
A related issue is the rotation matrix convention. I recall the
matrices given by LSQMAN and LSKAB were used to be transposed to each
other. But this time I found they were identical for the same NCS
transformation. Has one of these two programs changed its convention
lately?
Thanks for any help.
-------------------------------------------------
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: [EMAIL PROTECTED]
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Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
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