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venkataraman kabaleeswaran wrote:
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Hi everyone
I have used lsqkab and lsqman to superimpose related
molecules.
I would like to display the axis of rotation from the
rotation matrix
that was used by lsqman to superpose the two subunits.
I am also interested in calculating vectors for the
different rotation axes and their corresponding
rotation angles.
How can this be done? Any help would be greatly
appreciated.
Below is some perl code which converts a 3x3 matrix to a vector plus angle.
You can then draw the vector, (perhaps translated to the centre of mass)
in pymol with a cgo (
http://pymol.sourceforge.net/newman/user/S0500cgo.html#14_4 ) as seen in
fig2a in http://nar.oxfordjournals.org/cgi/content/full/32/18/5442
================
#!/usr/bin/perl
@[EMAIL PROTECTED];
$T=$m[0]+$m[4]+$m[8]+1;
if ($T>0.0005) {
print "Case 1: ";
$S=0.5/sqrt($T);
$w = 0.25 / $S;
$x=($m[5]-$m[7])/$S;
$y=($m[6]-$m[2])/$S;
$z=($m[1]-$m[3])/$S;
} else {
print "Case 2";
if (($m[0]>$m[4])&&($m[0]>$m[8])) {
print "a: ";
$S=sqrt( 1.0 + $m[0] - $m[4] - $m[8] ) * 2;
$x=0.5/$S;
$y=($m[1]+$m[3])/$S;
$z=($m[2]+$m[6])/$S;
$w=($m[5]+$m[7])/$S;
} elsif (($m[4]>$m[0])&&($m[4]>$m[8])) {
print "b: ";
$S=sqrt( 1.0 + $m[4] - $m[0] - $m[8] ) * 2;
$x=($m[1]+$m[3])/$S;
$y=0.5/$S;
$z=($m[5]+$m[7])/$S;
$w=($m[2]+$m[6])/$S;
# } elsif (($m[8]>$m[0])&&($m[8]>$m[4])) {
} else {
print "c: ";
$S=sqrt( 1.0 + $m[8] - $m[0] - $m[4] ) * 2;
$x=($m[2]+$m[6])/$S;
$y=($m[5]+$m[7])/$S;
$z=0.5/$S;
$w=($m[1]+$m[3])/$S;
}
}
$angle= 2*acos($w);
$angledeg=$angle*180/3.1415926;
print "$x $y $z $angledeg\n";
sub acos { atan2( sqrt(1 - $_[0] * $_[0]), $_[0] ) }
===============
Cheers,
Charlie
--
Dr Charles S. Bond University of Dundee Tel: +44-1382-388325
Honorary Lecturer Dow St, Dundee Fax: +44-1382-345764
BBSRC David Phillips Fellow DD1 5EH, Scotland [EMAIL PROTECTED]
School of Life Sciences http://stein.bioch.dundee.ac.uk/~charlie
