On Mon, Feb 2, 2009 at 11:08 AM, Angel Herraez <[email protected]> wrote:
> Interesting, Bob
>
> This suggests me some promising possibilities. Could your
> implementation be used for them, probably using some scripting?
>
> a) Moving a subset of the model. For example, moving a ligand out of
> its binding site, to coarsely simulate the unbound or approaching
> states. Or just a better display of a file containing several
> separate molecules (for ex, I could combine 4 nitrogen bases in a
> file like in 4-panel display as far as they are aligned to be seen
> from a similar perspective; the starting 4 files will likely have
> different coordinate systems, but the dragging allows nme to put them
> side by side)
>
All I'm doing here is adding mouse-based operations. What you describe
can already be done by script using rotateSelected and
translateSelected, which operate in molecular coordinates.
> b) Model superimposition/alignment.
> For instance, DeepView does alignment from 2 loaded pdb files, when
> you choose in both models the atoms that will be used for
> superimposition. Each of the 2 models is then translated and rotated
> around as a whole until those atoms positions match, The new
> coordinates can be saved, for both models separate or together in a
> single file. This allows for displaying two-state animations, like
> hemoglobin oxi-deoxi transition.
That was my thought with the "minimize measurements" -- the idea would
be to mark the correlating atoms using measurements (any number?) and
then let Jmol find the "best fit". This would obviously be easier than
a general best fit, as it gets input from the user as to what atoms
are associated.
>
> It would be important that after manipulation the new coordinates can
> be saved to disk.
write state
does this already.
>
> Separate:
> If I remember correctly, after "set picking draw" ALT_LEFT is already
> translating the objects. So, do you plan to have ALT_SHIFT_LEFT doing
> the same, or am I missing some difference?
SHIFT_LEFT does the translating of the entire set of points; ALT_LEFT
does just one point; I had left ALT_SHIFT_LEFT as a "reserved" option.
So the proposal is that in 11.8 ALT_SHIFT_LEFT and SHIFT_LEFT are the
same.
Rolf, what would be a suitable alternative to ALT_LEFT? It works so
nicely on the PC.
Maybe you can help me identify what keys we have available for dragging? I see:
case LEFT: rotateXY
case MIDDLE: zoomBy, rotateZBy
case SHIFT_RIGHT: // the one-button Mac folks won't get this gesture
case CTRL_ALT_LEFT:
/*
* miguel 2004 11 23
* CTRL_ALT_LEFT *should* work on the mac
* however, Apple has a bug in that mouseDragged events
* do not get passed through if the CTL button is held down
*
* I submitted a bug to apple
*/
[this should probably be checked again]
case CTRL_RIGHT: translateXYBy
case CTRL_SHIFT_LEFT: slabByPixels
case CTRL_ALT_SHIFT_LEFT: slabDepthByPixels
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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