Divakar, have you taken a look at
http://fusion.stolaf.edu/chemistry/jmol/xtalx.htm? This page only works
with some browers right now; it is very new. It doesn't do all you ask,
but it does show that Jmol is not "just for proteins." Note that you can
enter data there by hand, as you seem to require. You could certainly
adapt that page to do most of what you describe below, I think.
[EMAIL PROTECTED] wrote:
--Jmol would be useful for the
visualisation of such structures as well as of planes,
directions and defects in the lattice, if I could enter into it
any crystal structure.
You can certainly do that there, and you can also define planes and axes
and such (not in fractional coordinates yet, though).
I'm very close to implementing that, though, as well.
I could visualise these as 2D / 3D
models.
Everything on your screen is 2D. Not sure what you mean by that.
I need to enter these by hand since I do not have access
to electronic versions of crystal structure databases.
just start typing in that textarea. If you call up one of the .res files
and then click on [fileContents] you can have a good starting point.
Further,
suppose I am trying to understand some interface structures in
crystals. I would need to build a crystal that is essentially
composed of two perfect unit cells related to each other in a
particular way, sharing a common interface plane.
That would involve loading two files into Jmol (as separate "models")
and then only displaying certain unit cells in each.
Certainly doable.
But I do understand now that Jmol is built and specialised for
handling organic large molecule structures, and not for crystal
structures from materials science.
You are correct that Jmol has its roots in large molecular structures as
well as small organic models, but we are seeing a lot of recent
development that you may not be aware of. See, for example:
http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm
I'm sure part of the difficulty here is that really there are three "Jmols":
--the pubic release version 10.2, which you are now familiar with.
--the "trunk" development version 10.3, which has a few bug fixes.
--the "branch" development version 10.x, which has considerably more
functionality.
My work is focused on that last branch, 10.x, and I work almost
exclusively with the applet, so this new functionality is not showing up
in the application in terms of menus. Currently we have no realistic
plan for bringing the 10.x functionality into the "trunk" version any
time soon, although Miguel is working on that. So if the sort of
functionality you are interested in is in 10.x, feel free to use it. I
only ask that if you find bugs, you let me know.
Bob Hanson
-------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
