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
> >- - - - - - - - - - - - - - - - - - - - - - - - - - - */
> >
> >
> >-------------------------------------------------------------------------
> >SF.Net email is sponsored by:
> >Check out the new SourceForge.net Marketplace.
> >It's the best place to buy or sell services for
> >just about anything Open Source.
> >http://sourceforge.net/services/buy/index.php
> >_______________________________________________
> >Jmol-users mailing list
> >[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
>
>
>
>-------------------------------------------------------------------------
>SF.Net email is sponsored by:
>Check out the new SourceForge.net Marketplace.
>It's the best place to buy or sell services for
>just about anything Open Source.
>http://sourceforge.net/services/buy/index.php
>_______________________________________________
>Jmol-users mailing list
>[email protected]
>https://lists.sourceforge.net/lists/listinfo/jmol-users
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
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:
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
