Daniel, AH, I see... Absolutely! Quaternion rotation got broken in 11.9.36. Yes, when quaternions are used in rotations they are not supposed to be around the center of the selected atoms unless there is also a translation as well or an atom set is given as well. This is a bug.
By the way, you can now do that with the rotation matrix "r" directly (MOLECULAR is assumed for matrix rotations): rotate selected @r In addition, if you know where you want the model in the end, you can just do this: rotate @r translate @t #(rotate with TRANSLATE implies both SELECTED and MOLECULAR) where r is a matrix and t is a vector. This does a direct rotation (about the center) and translation to take the selected atoms to a new location. Very useful for superposition! This is at http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip and will be incorporated into Jmol 12.0.7 and Jmol 12.1.5. Bob ps -- and you can use those end-of-line backslashes if you want in Jmol as well. On Mon, Aug 16, 2010 at 9:36 AM, Daniel Lundin <daniel.lun...@molbio.su.se>wrote: > Hi, > > A couple of weeks ago I noticed that my scripts that rotates a structure > and translates it to align with another didn't work anymore in > 12.0.RC[34], but I never saw any replies (I suppose you were all busy > with other issues in the release candidates). Now when I try out 12.0.6 > they still don't work like in (e.g.) 11.9.23. The structure isn't > translated and whether it's rotated I can't tell. Are the command(s) > changed in any way? I can't tell from the documentation that they are. > > This is a snippet from my script that loads the pdb files and does the > rotation and translation: > > appendNew = true > load 2oc5.pdb > load append 1w68.pdb > select :A/2 > # 2oc5A - 1w68A (note that the line is continued; I've inserted the > # backslashes in the mail > r = [[ -0.59598154055, -0.32209352896, -0.73556900555 ], [ \ > 0.21345024134, -0.94661804765, 0.24156420749 ], [ -0.774109164, \ > -0.013039573237, 0.63291782384 ]] > rq = quaternion(r) > t = { 174.54968533, 75.782173371, 65.591095934 } > rotateSelected MOLECULAR @rq > translateSelected @t > > > /Daniel > > -- > Daniel Lundin > > Department of Molecular Biology & Functional Genomics > Arrhenius Laboratories for Natural Sciences > Stockholm University, SE-106 91 Stockholm, Sweden > > tel. +46 (0)8 16 41 95, mobile: +46 (0)708 123 922, fax. +46 (0)8 16 64 88 > > Email: daniel.lun...@molbio.su.se > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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