I have an idea I'd like you to think about:
set syncScriptTarget "appletID"
this defines the applet (a specific applet ID) or applets (">" or "*")
that are to receive the stream of user actions from the driver applet,
precisely like you were sending the scripts to those applets (as well as
the current one). It also delivers all mouse movements to the other
applet as well. This may be more than you want, Eric, but I think it's
about all I can do right now. EVERYTHING the user does (including
loading models) will be delivered. If you want a selective subset, then
what you need to do is bracket the command you use with "sync OFF" and
"sync ON" so that that particular command does not get delivered.
Bob
Eric Martz wrote:
>Yes, Bob, I think a subset may do the job.
>
>Again, the goal is to be able to align the two molecules
>(approximately) with sync off, and to zoom as needed to get the
>relevant portions to be approximately the same size. For example, if
>comparing a single domain model to a model with that domain plus
>another domain, the goal would be to zoom the models independently so
>as to make the common domain about the same size. In this case, one
>might also like to center the common domain, and perhaps hide the
>"other" domain.
>
>Then after turning sync on, the follower should rotate and zoom and
>translate according to the leader, but relative to the follower's
>initial position. The followers center should not be affected. More
>specifically:
>
>ROTATION
>What we want is for the follower to rotate relative to its initial
>position when sync was turned on, rotating the same relative angles
>as the leader. When the molecules are not aligned, we don't want the
>follower to rotate to the absoute angles (relative to the coordinate
>system) adopted by the leader.
>
>CENTER
>Movements of the leader should not change the rotation center of the follower.
>
>ZOOM
>Similarly, we want the follower to zoom relative to its initial zoom.
>So, suppose that when sync was turned on, the follower was at 150%
>zoom and the leader was at 100% zoom. If the leader is then zoomed to
>120%, I think we'd want the follower to zoom to (1.2)*(150%).
>
>Incidentally, I think that in the current implementation, only
>rotation triggers sending sync moveto commands. Specifically, in
>Windows, where you can zoom with the mouse wheel without any
>rotation, often the followers do not zoom until the leader is
>rotated. It would be good if pure zooming would also trigger sending
>sync moveto's.
>
>TRANSLATION
>Translation should be relative, like rotation. The follower should
>translate relative to its initial position, following translation of
>the leader relative to the leader's initial position.
>
>Since I want sync to do rotation, zoom, and translation, but relative
>to the starting orientation, I suggest that the new set command might be named
>
>set syncRelative on
>
>I would deem the current sync behavior to be "absolute".
>
>Thanks very much, -Eric
>
>At 12/11/07, you wrote:
>
>
>>interesting -- right, never thought of synching two different models.
>>Hmm.... The command being sent is this:
>>
>>moveto \
>>/* time, axisAngle */ 1.0 { 917 -188 -351 68.47} \
>>/* zoom, translation */ 100.0 0.0 0.0 \
>>/* center, rotationRadius */ {1.5 1.5 1.5} 2.8160255 \
>>/* navigation center, translation, depth */ {0.0 0.0 0.0} -17.803644
>>-20.691141 50.0;
>>
>>Now, I think what you are saying is that you want a subset of that.
>>Since there's one place in the code that generates this command and
>>sends it to the other applet, we could certainly modify that to suit.
>>What subset would you like? Maybe just the rotation part? That would be
>>easy enough. Something like
>>
>>set syncRotationOnly
>>
>>perhaps.
>>
>>
>>
>>Eric Martz wrote:
>>
>>
>>
>>>I am using sync in my Jmol Tutorial-Authoring Template (JTAT) when
>>>multiple molecules are displayed side by side. I send "sync * on" to
>>>only one Jmol, the last one. I think sync is very important, but
>>>there is one major inadequacy in the present implementation.
>>>
>>>The problem arises when comparing two different molecules. When the
>>>molecules being synched are not aligned in their coordinate systems
>>>(as is typically the case for independent crystallographic results),
>>>sync is not working satisfactorily. An example is View 5 in Chapter 3
>>>at the JTAT Demo
>>>(http://bioinformatics.org/jmol-tutorials/jtat/jtatdemo/ch_comp/cha
>>>
>>>
>>pter.htm )
>>
>>
>>>With Chime, you to move one molecule relative to the other (with
>>>synch off). Then, when you turn on synch, the relative orientation is
>>>maintained. Also each molecule rotates about its own center of mass,
>>>but in synch with the other(s). I think this is what is needed in Jmol.
>>>
>>>Perhaps a new Jmol command is needed to record the relative
>>>orientations, and maintain those in the sync'ed state? Also some
>>>mechanism is needed to rotate each molecule about its center of mass
>>>by default, rather than the other molecule's center of mass.
>>>
>>>Thanks, -Eric
>>>
>>>
>>>/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>>Eric Martz, Professor Emeritus, Dept Microbiology
>>>U Mass, Amherst -- http://www.umass.edu/molvis/martz
>>>
>>>Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
>>>Biochem 3D Education Resources http://MolviZ.org
>>>See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
>>>Protein Explorer - 3D Visualization: http://proteinexplorer.org
>>>Workshops: http://workshops.proteinexplorer.org
>>>World Index of Molecular Visualization Resources: http://molvisindex.org
>>>ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
>>>Atlas of Macromolecules: http://atlas.proteinexplorer.org
>>>PDB Lite Macromolecule Finder: http://pdblite.org
>>>Molecular Visualization EMail List (molvis-list):
>>> http://bioinformatics.org/mailman/listinfo/molvis-list
>>>- - - - - - - - - - - - - - - - - - - - - - - - - - - */
>>>
>>>
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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
>>
>>
>>
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>
>/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
>Eric Martz, Professor Emeritus, Dept Microbiology
>U Mass, Amherst -- http://www.umass.edu/molvis/martz
>
>Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
>Biochem 3D Education Resources http://MolviZ.org
>See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
>Protein Explorer - 3D Visualization: http://proteinexplorer.org
>Workshops: http://workshops.proteinexplorer.org
>World Index of Molecular Visualization Resources: http://molvisindex.org
>ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
>Atlas of Macromolecules: http://atlas.proteinexplorer.org
>PDB Lite Macromolecule Finder: http://pdblite.org
>Molecular Visualization EMail List (molvis-list):
> http://bioinformatics.org/mailman/listinfo/molvis-list
>- - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
>-------------------------------------------------------------------------
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>It's the best place to buy or sell services for
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>_______________________________________________
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>[email protected]
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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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