On Feb 15, 2006, at 7:01 p, Bob Hanson wrote:
[EMAIL PROTECTED] wrote:
The same approach could also be used to build the script for a
full dump. Instead of using the selected atoms, the atoms with the
same properties could be grouped in a first step. Then the
described approach could be used for each of these groups. I know
that I have simplified things, but I just wanted to present the
general idea.
It's certainly an interesting challenge -- the goal, to provide a
"snapshot" of the state of the system. There are two logical
approaches I can think of:
a) a record of scripts run.
b) a dump of properties for every single atom, preferably grouped
into sets.
The Script Recorder in Protein Explorer was built to accomplish this
very task, albeit using Chime instead of Jmol.
we chose, by necessity, option a. essentially, every command issued
by the user in PE is captured, filtered (along with the feedback from
Chime), and saved in a history. there is also some additional
control on top of this automated process, to deal with situations
like duplicate commands, etc.
The problem, of course, is not saving or replaying commands - which
is fairly fast - but the number of false starts and dead-ends that
the typical user encounters while setting up a view. if you actually
read the output script from PE, it quickly becomes impossible to tell
what it will render in the end. but, running the script back in PE
works rather well. so, one question would be: do you care about the
cleanliness of the output script? do you want it to be 'human-
readable' in other words? if not, the simplest method is brute force
- just save every command that comes in. of course, you would have
to do some rudimentary error-checking so a typo didn't bonk your
saved script.
on a more sophisticated level, if Jmol is storing descriptive data
for each atom - color, format, etc. - then it should be fairly
straightforward to have it output a clean, set-based script to
regenerate the view.
this topic came up a while ago, on-list I believe, and Miguel said
something like he would rather work on implementing solvent-
accessible surfaces then this feature... :-)
regards,
tim
--
Timothy Driscoll em: [EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
<http://www.molvisions.com/> im: molvisions
usa:virginia:blacksburg tx: [EMAIL PROTECTED]
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