On Fri, Jun 1, 2012 at 12:17 PM, Andrew Long <andrew.long.3...@gmail.com>wrote:
> So I've created a program that colors the colixs inside the mesh of a
> surface like so. Is it possible to save the state with the colixs set? So
> far when I've tried to save it the surface just comes out orange. Is there
> a flag I can set to get Jmol to save the Colix data? It would be nice if I
> could just save the results and surfaces as one file that I can easily
> share instead of having to parse the 700-2600 output files each time I want
> to generate the surface again.
>
>
If you did it right, just
write xxx.jvxl
should save all the color information. Then you can read that JVXL file and
save the full state. Now you have a state that references the JVXL file
with the proper mapping.
> Secondly I've been working on a helpful tool bar that would mimic the
> builder tool bar from popular computational kits such as Gaussian and
> Spartan to help me understand how Jmol works.
That sounds terrific. I would love to see that working. ModelKitMode was
just my attempt at getting something reasonably useful. This sounds WAY
better.
> I've reimplemented most of what the model kit mode does so far with the
> addition of a helpful window that lets you see what fragment will be
> added. I'd like to improve it by allowing any fragment to be added to
> current model after selecting any terminal atom on the fragment and then
> selecting terminal atom on the model. Unfortunately I've been having a
> difficult time parsing the actionmanager. Has anyone writen up a helpful
> guide that explains how it works and in particular what strings correspond
> to what actions? many of the command strings seem to be scattered and at
> times hard to find for someone who isn't familiar with Jmol. Most of what
> I've figured out so far has been from reading the code and using
> System.out.println loops to figure out whats going on.
>
>
That's the way it's done. Sorry. Read the code; figure it out. I admit that
the processing of all the actions is pretty complex and rather arbitrary.
There can be some surprises there if you are trying to unbind and rebind
mouse actions to scripts. You sure you need that? Why not just use
mouse-action "sync" callbacks to track what's being done?
You are probably the first to hack into that code. Good luck. I don't
exactly see why you feel you need to do that. The ActionManager code is not
something you want to be adjusting. In any case, if you do that, please
subclass ActionManager, don't just hack its methods.
Also is it possible to have the currently selected atom to be highlighted?
> I've been trying to find a graceful way to do that without mangling the
> code.
>
>
you mean
selectionHalos on
?
> Thanks again!
>
> Cheers Andrew
>
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--
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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