Hi Bob, I'd like to use this with two side-by-side applets where I am syncing the mouse movements using sync * on; sync * "set syncMouse true" http://moleculesinmotion.com/aminoacids/ (Surface coloring not correct yet, please ignore.)
Each applet loads an amino acid from a drop-down menu. I have used a moveto command to orient their initial positions. It looks to me like I want permutation #6 from your list, but I am not sure how to do this between two different applets. Can you help? Frieda ////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 ////////////////////////////////////// On Aug 15, 2008, at 10:23 AM, Bob Hanson wrote: > [blogging here] > > You ask -- What the heck are these quaternions? Here's an example of > where quaternions come in handy in Jmol. > > Say you have two files that you want to display sequentially, 1.xyz > and > 2.xyz. They are connected in some way, perhaps because they are two > files along the same mechanistic pathway. When the user clicks a > link to > switch from Model 1 to Model 2 you want the user to experience no jump > of orientation -- just a subtly different file. How can that be done? > > 1) Well, if the two files have the same basic coordinates, there's no > real problem. You just use > > load 1.xyz > ...user changes orientation... > save orientation; > load 2.xyz > restore orientation; > > The save/restore orientation does the trick. > > 2) But what if the INITIAL orientations of the two models are > different? > That is, what if generally you might have to use > > load 2.xyz > moveto .... > > to make 2.xyz line up with 1.xyz? What then? The problem is that if > the > user has manipulated the model, you can do that restore to get back to > THEIR orientation, but that's for the wrong model, and you can't just > put the restore before the moveto command, because the moveto will > override that. What to do? > > 3) The solution is to use quaternions. Jmol can report its rotational > state in terms of a quaternion. All you do is: > > q1 = script("show rotation") > > That's it. You now have saved the rotational state. AND, Jmol can now > rotate any model by that quaternion: > > rotate @q1 > > So, to apply a user's changes to a DIFFERENT model: > > load 1.xyz > ...user changes orientation... > q1 = script("show rotation") > load 2.xyz > moveto 0.0 ... > rotate @q1 > > This is different. It saves the user's changes as a quaternion and > then > applies that quaternion after the moveto. Provided you have used 0 > seconds for the time on that moveto, you won't even see a flicker with > Jmol 11.6.RC7 (this was recently fixed). > > 4) Ah, but there's a catch! The catch is that the user also may have > changed the zoom or the translation. The solution again uses > quaternions, but this time in combination with save/restore. > Quaternions > encode the rotation of a model in a RELATIVE SENSE. Thus, if > > q1 = [first rotational state] > q2 = [later rotational state] > > then the division > > q3 = q2 / q1 > > gives you the CHANGE in going from the first state to the second > (sometimes referred to as the "quaternion difference" or "quaternion > derivative"). > > So, check this out: > > load 1.xyz > ...user changes orientation... > q1 = script("show rotation") > save orientation o1; > load 2.xyz > moveto 0.0 ... > q2 = script("show rotation") > restore orientation o1; > rotate @{q2 / q1} > rotate @q1 > > See what that does? We are saving: > > q1 the user's current rotation of model 1 > o1 the user's full orientation change, including rotation q1, zoom, > and translation > q2 our "default" rotation for model 2 > > The restore takes us to rotation q1 and applies any user zoom or > translation changes. > The first rotation takes us back to our default rotation for Model > 2, q2. > The second rotation applies the change the user made. > > By the way, sequential rotations are applied using LEFT > multiplication. > Those two rotations can be combined as: > > rotate @{q1 * q2 / q1} > > That's called a similarity transform. > > 5) Now, what if you have to rotate BOTH files to get the default > orientation you want? Then it's a bit more tricky, but not too bad: > > load 1.xyz > moveto 0.0 ... > q1a = script("show rotation") > ...user changes orientation... > q1b = script("show rotation") > save orientation o1; > load 2.xyz > moveto 0.0 ... > q2 = script("show rotation") > restore orientation o1; > rotate @{q2 / q1b} > rotate @{q1b / q1a} > > See what that does? We are saving: > > q1a our "default" rotation for model 1 > q1b the user's current rotation of model 1 > o1 the user's full orientation change, including rotation q1b, > zoom, > and translation > q2 our "default" rotation for model 2 > > The restore takes us to rotation q1b, along with the user's changes to > translation and zoom. > The first rotation takes us back to our default rotation for Model 2, > q2, but leaves the user's zoom and translation unchanged. > The second rotation applies the change the user made relative to our > default for Model 1. > > > 6) Finally, what if we want to allow the user to switch back and forth > between models with NO orientation jump? This is really cool. Here > you go: > > First, load an initial file: > > load 1.xyz > moveto 0.0 ... > q = script("show rotation") > > > Then any later load of ANY file looks like this: > > qrel = quaternion(script("show rotation")) / q > save orientation o1; > load xxx.xyz > moveto 0.0 ... > q = script("show rotation") > restore orientation o1; > rotate @{qrel * q / quaternion(script("show rotation"))} > > and now the code is fully symmetric. Put in any file name for > "xxx.xyz", > and this code will preserve orientation based on a custom default > rotation. > > 7) Summary > > Quaternions encode rotations. Their multiplication represents a series > of rotations, and their division represents changes made to rotational > states. Jmol web page developers can use quaternions to record > customized defaults as well as changes the user has made to those > defaults. These changes can then be applied to OTHER models so as to > create a seamless transition from one model to another. > > > Bob > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > 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 > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
