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jeffrey Offline OP
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Dear all,

I would like to know how CHARMM calculate the coordinates of a new conform after using COOR ORIENT. The following steps are followed in CHARMM:

------
read top
read par
read psf

read coor A1
read coor comp A2

coor orient mass rms sele type ca .or. type n .or. type o .or. type c end
write coor A3
-----------------

Some output is as follows:
==============
CENTER OF ATOMS BEFORE TRANSLATION -0.06678 0.08931 -0.14376
CENTER OF REFERENCE COORDINATE SET 4.26786 12.51933 -0.17027
NET TRANSLATION OF ROTATED ATOMS 4.33464 12.43002 -0.02650
ROTATION MATRIX
-0.927345 0.265354 -0.263854
-0.043213 0.624446 0.779872
0.371704 0.734612 -0.567610
AXIS OF ROTATION IS 0.063931 0.897742 0.435858 ANGLE IS 159.27
CENTER OF ROTATION 1.602891 6.477258 -0.440226 SHIFT IS 11.424516
===============

Could someone please tell me how CHARMM calculate the coordinates of A3 from these of A1 using the above output?

Thanks very much for your time.

Have a nice day.
-------
Jeffrey

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rmv Online Content
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A1 is rotated and translated to minimize the mass-weighted RMSD between the selected atoms in A1 and the corresponding atoms in A2.

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jeffrey Offline OP
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Hi Rick, Thanks. Do you mean that:

ROTATION MATRIX*A1+NET TRANSLATION OF ROTATED ATOMS
= A3 ?

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jeffrey Offline OP
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Hi, I think I find out the results. It should be

(A1-CMA1)*ROTATION MATRIX + CMA2 = A3

where CMA1 is the center of mass of A1 conform (center of atoms before translation), the mobile conform; CMA2 is the center of mass of A2 conform (center of mass of reference coordinate set), the reference structure.

The corresponding .src is rotlsq.src

-----
Jeffrey

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First the translation is removed (trivial operation), then the least-squares rotation is applied
A3=ROTATION*(A1-TRANSLATION)


Lennart Nilsson
Karolinska Institutet
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How can I get the translation vector components and rotation matrix values so I can apply the same coordinate transformation to an arbitrary vector (or point)?

For example, I may have the velocity of a certain atom (vx,vy,vz) which I want to transform in the same way as the COOR ORIE did to the original coordinate set. In other words, how can I get the ROTATION matrix and TRANSLATION vector values within a CHARMM script?

Thanks.

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rmv Online Content
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Some Fortran coding may be required to achieve this; as far as I can tell from corman.doc and subst.doc, only the rotation axis is stored in ? variables.


Rick Venable
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I can think of a number of applications for which it would be really useful for CHARMM to output this information at a certain PRNLEV.

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rmv Online Content
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A check of recent source code (source/corman2.src, routine ORINTC) indicates the translation vector is stored in ?XMOV, etc. and that the rotation angle is stored in ?THET


Rick Venable
computational chemist


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