On May 11, 2007, at 7:46 AM, Bob Hanson wrote: > 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. > hi Bob,
thanks for the explanation. that did indeed make sense, helped a lot, and worked...up to a point. I translated the atoms in the original structure, applied the matrix, and ended up with the same distance as I see between equivalent atoms in the transformed structure: original ATOM 1 ATOM 2 d(2-1) M*d x 3.95 3.86 -0.08 -1.25 y 38.05 36.58 -1.48 0.59 z 17.44 17.32 -0.11 0.53 transformed ATOM 1 ATOM 2 d(2-1) x 52.94 51.69 -1.25 y 50.01 50.6 0.59 z 89.41 89.95 0.53 that's good, but now I'm stuck. unapplying the translation does not get me to the transformed coords. this makes me think that... > Unless they also applied a zoom.... > but I have no other data from the operation other than the matrix, and the two coordinate sets. tim -- Timothy Driscoll em: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksburg, VA 24061 04-16-07. We will not forget you. ------------------------------------------------------------------------- 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
