what you will need to know are two points in each case, not one. What you don't know or aren't figuring in is the possibility that the origin has been shifted. Rotation requires a center. Maybe it's (0,0,0), maybe not. In Jmol what we have to do is:
1) apply a translation to set the "center of rotation" at (0,0,0) 2) apply the rotation 3) unapply the translation to set the center of rotation where it belongs The fact that your two atoms have different distances to (0,0,0) suggests immediately that you cannot skip steps (1) and (3). If you take instead the difference in coordinates between any two atoms, then you should see the rotation working. You've only supplied one coordinate from each, so I am sticking my neck out here, but I suspect that if you were to take the two data sets and in each case choose an arbitrary atom -- perhaps this one would do -- and subtract off that coordinate from every atom coord in its own set, so that these two each read (0,0,0) (and thus themselves automatically fulfill the matrix transformation), then you will see the expected relationship. The only question then is whether they left- or right-multiplied the matrix. Unless they also applied a zoom.... That make sense? Bob Timothy Driscoll wrote: >On May 11, 2007, at 1:37 AM, Bob Hanson wrote: > > > >>See if by any chance going the other way works -- from the verified >>coordinates to the original. If that's the case, then you need the >>inverse of this matrix. >> >> >> >> >yeah, I've been trying stuff like this, kinda haphazardly, without >luck. for example: > > >coords before transformation: >ATOM 1 N PRO 6 3.948 38.053 17.436 1.00 >41.27 N > > >coord after transformation: >ATOM 1 N PRO B 6 52.942 50.009 89.414 1.00 41.27 > > >the matrix: > > 0.58 0.805 0.125 > 0.521 -0.484 0.703 > 0.626 -0.342 -0.7 > > > > > > >>Timothy Driscoll wrote: >> >> >> >>>On May 10, 2007, at 3:54 PM, Bob Hanson wrote: >>> >>> >>> >>> >>>>This is always a royal pain to get right. Certainly looks like a >>>>rotation matrix to me. >>>>It's got the right form. My guess is you put the vector on the >>>>right and >>>>multiply as: >>>> >>>>x' = m11*x + m12*y + m13*z >>>> >>>>across the top row of that matrix. Likewise for y' across the >>>>second. >>>> >>>> >>>> >>>> >>>> >>>that does not appear to work, no, and that's what confuses me. >>>(MUSTANG also outputs a pdb file with the aligned coordinates, which >>>I use as verification.) I've been trying to read some literature on >>>transformation matrices but most of them are 4x4, not 3x3? >>> >>>anyway, I'll keep looking. >>> >>>tim >>> >>> >>> >>> >>> >>> >>>>Timothy Driscoll wrote: >>>> >>>> >>>> >>>> >>>> >>>>>hi, >>>>> >>>>>I have two structures that I have aligned using a program called >>>>>MUSTANG. the program gives me a 3x3 transformation matrix like >>>>>this >>>>>one: >>>>> >>>>> 0.58 0.805 0.125 >>>>> 0.521 -0.484 0.703 >>>>> 0.626 -0.342 -0.7 >>>>> >>>>> >>>>>in order to superimpose my second structure onto the coordinate >>>>>system of the first, I am told that I should apply this matrix >>>>>to the >>>>>xyz coords of the second. I thought this could be done via a >>>>>simple >>>>>matrix multiplication, but apparently not. >>>>> >>>>>can anyone please suggest a reference that deals with this? >>>>> >>>>> >>>>> >>>>>thank you, >>>>> >>>>>tim >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>-------------------------------------------------------------------- >>>>-- >>>>--- >>>>This SF.net email is sponsored by DB2 Express >>>>Download DB2 Express C - the FREE version of DB2 express and take >>>>control of your XML. No limits. Just data. Click to get it now. >>>>http://sourceforge.net/powerbar/db2/ >>>>_______________________________________________ >>>>Jmol-users mailing list >>>>Jmol-users@lists.sourceforge.net >>>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>>> >>>> >>>--------------------------------------------------------------------- >>>---- >>>This SF.net email is sponsored by DB2 Express >>>Download DB2 Express C - the FREE version of DB2 express and take >>>control of your XML. No limits. Just data. Click to get it now. >>>http://sourceforge.net/powerbar/db2/ >>>_______________________________________________ >>>Jmol-users mailing list >>>Jmol-users@lists.sourceforge.net >>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>> >>---------------------------------------------------------------------- >>--- >>This SF.net email is sponsored by DB2 Express >>Download DB2 Express C - the FREE version of DB2 express and take >>control of your XML. No limits. Just data. Click to get it now. >>http://sourceforge.net/powerbar/db2/ >>_______________________________________________ >>Jmol-users mailing list >>Jmol-users@lists.sourceforge.net >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > >tim > > ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. 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