Op dinsdag 04 februari 2003 17:59, schreef Miguel:
> > Is it possible to extend the capabilities of the Jmol applet to read
> > shelx97 files as the version 5 application can?
> > It looks like the Jmol-applet.jar has the ShelxReader.class in it!
> We plan to release Jmol version 6 within the next few weeks.
> One of the goals of this release is to support more file formats.
> I have not been working on file formats, so I am not sure. But unless
> there is some great obstacle, support for this file format will be in this
> release. I will check with one of the crystalography people to confirm.
there were some issues why the next applet (the upcoming 6 version) currently
does not have ShelX support, but I'll try to resolve those.
> > How about the various measurement capabilities?
> Well, the measurement capabilities *will* be in the next release of the
> applet, but they may not be that easy to get to.
> For this release we have put in rather broad support for RasMol/Chime
> scripting. Thus, from a script you can create a measurement between atoms
> (the RasMol scripting language uses the term "monitor").
> However, for this release we do *not* plan to have user-interface gestures
> which would allow a user to apply measurements interactively with the
> mouse. This will need to wait for the next release.
> > And it would be nice if
> > the measurements could take into account the uncertainties in the
> > atomic co-ordinates (this info is available in the shelx file) so Jmol
> > could calculate the uncertainties in the geometrical parameters.
> I am not a chemist, let along a crystalographer, so I am not sure I
> understand the problem/question.
> Is it the case that you want:
> distance 1.523 +/- .05 angstroms
> angle 45 +/- 4 degrees
I've been discussing this last week, and a future Jmol version will be
able to colour atoms based on their B factor, much like it can already
colour atoms by it's partial atomic charge.
Actual display as those special eliptic atoms (of which I forgot the name)
is much more difficult... For that we would need an example algorithm on
how to calculate those for 3D display that can still rotate... I do not think
that the current developers have the ability to do that... (ofcourse we would
welcome such contributions...)
> > This
> > would be very valuable to chrystallographers like myself especially if
> > it were available in the Jmol applet and users of facilities like mine
> > could do those calculations over the web!!
> Part of our goal is to make the applet more robust. As we add
> functionality we want to enhance both the application and the applet.