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Hi Eleanor,
Thank you for looking into this in details. I have checked your scripts
against the ones I used and rerun DM through either scripts or CCP4i with
three NCS-symmetry input options: ROTA EULER, ROTA MATRIX and OMAT.
Results are summerized below:
1. DM gave high correlation after averaging when NCS-symmetry was input as
either Euler angles or rotation/translation from LSQKAB, whether running
through scripts or GUI. When I used ROTA MATRIX in my script previously I
forgot to change keyword from COMBINE FREE to COMBINE PERT. The old
keyword FREE caused poorer correlation.
2. Running DM with OMAT option gave me low correlation values if I
provided rotation matrix components as reported by LSQMAN(see my previous
email attached). DM gave high correlation ONLY IF the LSQMAN rotation
matrices of B to A (and C to A) were given in combination of the LSQMAN
translation of A to B (and A to C). This seems to me that with OMAT
option DM is still expecting the rotation matrix that is TRANSPOSE to the
LSQKAB matrix convention. This is the case no matter running DM with
script or through GUI.
3. I need to take back my claim that the NCS between 3 molecules in the
asymmetric unit of P21 space group is 2-fold. Actually only the NCS from B
to C is 2-fold with the following LSQMAN matrix:
B to C
Rotation : -0.01950950 0.62457961 -0.78071737
0.61690730 -0.60697758 -0.50100249
-0.78679395 -0.49140459 -0.37346587
Translation : -99.6547 82.4475 -58.2044
This matrix is close to symmetrical therefore the transpose/inversion is
itself as pointed out in Ian's message. But the NCS from A to B (and A to
C) is NOT 2-fold as indicated by their non-symmetrical matrices. These
matrices are not identical to their transpose. Sorry that if my previous
message caused any confusion.
4. Now it comes to my original question: why the rotation matrices printed
for A to B (or A to C) by both LSQMAN and LSQKAB are now the SAME instead
of being TRANSPOSE to each other as in the past. It seems to me DM expects
an OMAT that is transposed to LSQKAB matrix. If LSQMAN has adapted the
convention identical to the LSQKAB(not clear to me if this's the case
from the USF web page, http://xray.bmc.uu.se/usf/lsqman_man.html#H80), DM
needs to be updated.
I hope this did not cause any more confusion.
-------------------------------------------------
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 Mon, 16 Jan 2006, Eleanor Dodson wrote:
Hmm - I cant reproduce this: All these give virtaully the same
anser - as they should..
I took the outputs from LSQKAB
ROTATION MATRIX
0.918 0.374 0.131
0.345 -0.590 -0.730
-0.196 0.715 -0.671
PATTERSON SPHERICAL POLARS OMEGA PHI CHI OMEGA TO AXIS ZO PHI
FROM AXIS XO TO AXIS YO
WHEN BETA=0 CAN ONLY DEFINE ALPHA + GAMMA .
WHEN BETA = 180 CAN ONLY DEFINE GAMMA - ALPHA.
CROWTHER ALPHA BETA GAMMA 100.18892 -132.15184 -105.30077
SPHERICAL POLARS OMEGA PHI CHI 91.13347 12.74478 132.20241
DIRECTION COSINES OF ROTATION AXIS 0.97517 0.22057
-0.01978
Angle between rotation axis and Centroid vector 44.18956
THE TRANSLATION VECTOR IN ANGSTROMS ALONG THE ORTHONORMAL
AXES IS
-45.32019 42.44644 14.94666
Then ran DM in turn with the euler angle contention, polar angle and
rotation matrix.
All translations are the same of course.
Euler angle command script:
*****************************************************************
/tmp/ccp4/testing_208_1_com.tmp
*******************************************************************
mode -
SOLV -
AVER
combine PERT
scheme ALL
ncycles -
AUTO
solc 0.5
average -
REFI
rota EULER -
0.0 0.0 0.0
tran 0.0 0.0 0.0
average -
REFI
rota EULER -
100.18892 -132.15184 -105.30077
tran -45.32019 42.44644 14.94666
ncsmask
LABIN FP=F_id232 SIGFP=SIGF_id232 PHIO=PHIC FOMO=FOM
LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM
RSIZE 80
END
Polar angle one:
mode -
SOLV -
AVER
combine PERT
scheme ALL
ncycles -
AUTO
solc 0.5
average -
REFI
rota POLAR -
0.0 0.0 0.0
tran 0.0 0.0 0.0
average -
REFI
rota POLAR -
91.13347 12.74478 132.20241
tran -45.32019 42.44644 14.94666
ncsmask
LABIN FP=F_id232 SIGFP=SIGF_id232 PHIO=PHIC FOMO=FOM
LABOUT FDM=FDMp PHIDM=PHIDMp FOMDM=FOMDMp
RSIZE 80
END
And rotation matrix:
*******************************************************************
/tmp/ccp4/testing_210_1_com.tmp
*******************************************************************
mode -
SOLV -
AVER
combine PERT
scheme ALL
ncycles -
AUTO
solc 0.5
average -
REFI
rota MATRIX -
1.0 0.0 0.0 -
0.0 1.0 0.0 -
0.0 0.0 1.0
tran 0.0 0.0 0.0
average -
REFI
rota MATRIX -
0.918 0.374 0.131 -
0.345 -0.59 -0.73 -
-0.196 0.715 -0.671
tran -45.32019 42.44644 14.94666
ncsmask
LABIN FP=F_id232 SIGFP=SIGF_id232 PHIO=PHIC FOMO=FOM
LABOUT FDM=FDMr PHIDM=PHIDMr FOMDM=FOMDMr
RSIZE 80
END
Huiying Li wrote:
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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
*** For details on how to be removed from this list visit the
***
*** CCP4 home page http://www.ccp4.ac.uk ***
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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