OK, Jmol 11.3.57 is ready for release. Eric, I hope you will take a look
at it when Nico releases it. I think it will do nicely.
sync . ON; sync > slave #one driver, rest are receivers only
set syncMouse FALSE; set syncScript FALSE # sync orientation only (using
!moveto commands)
set syncMouse TRUE; set syncScript FALSE # sync the mouse movements --
not scripts
set syncMouse FALSE; set syncScript TRUE # sync all script commands,
not mouse movements
set syncMouse TRUE; set syncScript TRUE # sync all script commands and
mouse movements
I think the second of these matches the CHIME business closely. Every
motion should track perfectly, including all mouse-based motions
including rotating about x, y, and z, rotating just one molecule,
zooming using shift-drag, zooming using the mouse wheel, and translation
using alt-shift-drag.
Note that if you have multiple drivers, as with
sync * ON
Note that you can't have multiple drivers with set syncMouse TRUE --
that wouldn't make any sense. In contrast, with set syncScript TRUE, you
can have multiple drivers.
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
>- - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
>-------------------------------------------------------------------------
>SF.Net email is sponsored by:
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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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