Oh, you can also do that entirely within Jmol scripting, by the way, :
If you are not synchronizing and you want to TRANSFER the orientation
from one applet to another, and, as you are doing, you have your own
customized initial orienation, then what you have to do is first query
that applet for qrel and its orientation:
var qrel = quaternion(javascript("jmolEvaluate('quaternion(script(\"show
rotation\")) / q','A')"))
var o = javascript("jmolEvaluate('script(\"show orientation
moveto\")','A').replace(/1.0/,'0.0')")
load xxx.xyz
moveto 0.0 ...
q = script("show rotation")
script inline @o
rotate @{qrel * q / quaternion(script("show rotation"))}
Bob Hanson wrote:
>Not a problem, Frieda. Whether you have one applet or four, it's all the
>same, provided they are mouse-synchronized.
>
>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"))}
>
>
>
>Just make sure that "q=" line is in your script when you INITIALLY load
>a model into any applet.
>When you go to reload the applet, use the other set.
>
>OR, I think you could do a test and see whether there's already a model
>there or not:
>
> var haveModel = (_currentModelNumberInFile != 0)
> if (haveModel)
> qrel = quaternion(script("show rotation")) / q
> save orientation o1;
> endif
> load xxx.xyz
> moveto 0.0 ...
> q = script("show rotation")
> if (haveModel)
> restore orientation o1;
> rotate @{qrel * q / quaternion(script("show rotation"))}
> endif
>
>
>
>
>This works because you are synchronizing.
>
>If you are not synchronizing and you want to TRANSFER the orientation
>from one applet to another, and, as you are doing, you have your own
>customized initial orienation, then what you have to do is first query
>that applet for qrel and its orientation:
>
>[javascript here, presuming that was created as "A" -- there is an
>applet with ID jmolAppletA]
>
> var qrel = jmolEvaluate('quaternion(script("show rotation")) / q', "A")
> var o = jmolEvaluate('script("show orientation moveto")',
>"A").replace(/1.0/,"0.0")
>
>Then build a script command that does the SECOND part of the above sequence:
>
> var script = 'load ' + someFileName + ';moveto 0.0 ...;q =
>script("show rotation");' + \
> o + ';rotate @{quaternion('+qrel+') * q /
>quaternion(script("show rotation"))};sync . on'
>
>Then send that script to the other applet. We don't need the
>save/restore, because the "o" variable will hold the orientation in it
>as a moveTo command. We are defining qrel in the JavaScript, so we just
>insert it where needed. Since it is in the form {xx xx xx xx}, we wrap
>it with the quaternion() function so that Jmol reads it properly as a
>quaternion.
>
>Bob
>
>
>
>
>
>
>
>
>Reichsman Frieda wrote:
>
>
>
>>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
>>>
>>>
>>>
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>>>
>>>
>>-------------------------------------------------------------------------
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>>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
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>>
>>
>>
>
>
>
>
--
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
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