> Looks to me like that first matrix you have there is not a standard
> rotation-translation matrix. Where does that come from?
>
> What is an "external tool"?
The external tool is tmalign.
tmalign 1qo2.pdb 1thf.pdb -o TM.sup -m matrix.txt
matrix.txt looks like:
-------- Rotation matrix to rotate Chain_1 to Chain_2 ------
m t(m) u(m,1) u(m,2) u(m,3)
1 42.0337552974 0.8034720298 0.2078260117 -0.5578898154
2 47.4497034560 -0.2191039598 -0.7680942401 -0.6016848786
3 27.8100634352 -0.5535577224 0.6056728385 -0.5716067360
Code for rotating Chain_1 from (x,y,z) to (X,Y,Z):
do i=1,L
X(i)=t(1)+u(1,1)*x(i)+u(1,2)*y(i)+u(1,3)*z(i)
Y(i)=t(2)+u(2,1)*x(i)+u(2,2)*y(i)+u(2,3)*z(i)
Z(i)=t(3)+u(3,1)*x(i)+u(3,2)*y(i)+u(3,3)*z(i)
enddo
I moved column 1 to the end and added a 4th row if 0,0,0,1
In PyMOL this 4x4matrix works fine.
> Also, are you sure the rotation-translation matrix you
> have there is the
> one that relates "a" to "b" and not just "a" to put its
> center of mass at
> {0 0 0}?
Uh, good question but wouldn't PyMol also then fail?
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