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Ian is right, the NCS symmetry between 3 copies of molecules is
indeed 2-fold(see the matrices below). This clears my confusion on the
way LSQMAN and LAQKAB print their rotation matrices.
However, my question on DM got unanswered: why DM gave good results
only if I provided NCS symmetry with EULER angles but failed with the
rotation matrix input(I have tried either ROTA MATRIX or OMAT options
assuming program handles them differently, also tried running script and
CCP4i GUI separately).
LSQMAN
A to B
Rotation : 0.35659924 0.89497125 0.26807317
0.79405671 -0.44152504 0.41776711
0.49225062 0.06388988 -0.86810553
Translation : -29.6767 98.3395 -116.3953
A to C
Rotation : 0.09560259 -0.34010872 0.93551391
-0.50114429 0.79558092 0.34044895
-0.86006665 -0.50137526 -0.09438394
Translation : 54.2229 62.6560 -40.8627
B to A
Rotation : 0.35659924 0.79405671 0.49225062
0.89497125 -0.44152504 0.06388988
0.26807317 0.41776711 -0.86810553
Translation : -10.2088 77.4156 -134.1709
C to A
Rotation : 0.09560259 -0.50114429 -0.86006665
-0.34010872 0.79558092 -0.50137526
0.93551391 0.34044895 -0.09438394
Translation : -8.9288 -51.8938 -75.9142
LSQKAB
A to B
ROTATION MATRIX:
0.35660 0.89497 0.26807
0.79406 -0.44152 0.41777
0.49225 0.06389 -0.86811
TRANSLATION VECTOR IN AS -29.67671 98.33947 -116.39539
CROWTHER ALPHA BETA GAMMA 57.31251 150.23941 172.60495
A to C
ROTATION MATRIX:
0.09560 -0.34011 0.93551
-0.50114 0.79558 0.34045
-0.86007 -0.50137 -0.09438
TRANSLATION VECTOR IN AS 54.22293 62.65603 -40.86268
CROWTHER ALPHA BETA GAMMA 19.99734 95.41594 -30.24002
B to A
ROTATION MATRIX:
0.35660 0.79406 0.49225
0.89497 -0.44152 0.06389
0.26807 0.41777 -0.86811
TRANSLATION VECTOR IN AS -10.20886 77.41563 -134.17094
crowther alpha beta gamma 7.39520 150.23941 122.68763
C to A
ROTATION MATRIX:
0.09560 -0.50114 -0.86007
-0.34011 0.79558 -0.50137
0.93551 0.34045 -0.09438
TRANSLATION VECTOR IN AS -8.92881 -51.89373 -75.91429
crowther alpha beta gamma 30.24002 -95.41593 -19.99773
-------------------------------------------------
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]
--------------------------------------------------
On Fri, 13 Jan 2006, Ian Tickle wrote:
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Maybe it's an NCS 2-fold? A 2-fold rotation matrix is its own
inverse/transpose (because you get the same result rotating +180 as
-180, which is obviously not true for any other axis order) so the CCP4
& O matrices would be the same for that special case!
-- Ian
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Gerard DVD Kleywegt
Sent: 13 January 2006 09:32
To: Huiying Li
Cc: CCP4 Bulletin Board; Gerard Kleywegt
Subject: Re: [ccp4bb]: DM and rotation matrix convention
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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?
http://xray.bmc.uu.se/usf/lsqman_man.html#H8
--dvd
******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of
Sciences] Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
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