On 2010-08-18 09:24, Robert Hanson wrote: > 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 > Thanks Bob, this worked like a charm...
> 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) > though this didn't. I can't find any error messages that seems to relate to this issue, it looks like the command just silently fails and the structure is not moved. Otherwise this is perfect for my purpose, which is just superposition from data from an alignment program (matrix and vector). As long as the two command works it doesn't matter so much though (my scripts are auto generated). > 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 > /Daniel > 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 > <[email protected]>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: [email protected] >> >> >> ------------------------------------------------------------------------------ >> 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 >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > > > ------------------------------------------------------------------------------ > 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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: [email protected] ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
