Re: [Jmol-developers] Load pmesh and load file in Jmol

Bob Hanson Thu, 16 Dec 2004 17:45:46 -0800

I'm putting in my pitch for the ONE THING I see missing in Jmol -- the capability of showing simplistic non-pmesh-file-based "electrostatic potential maps" for molecules. Chime makes an attempt at this -- really not satisfactory in my opinion -- but it does give SOME indication of electron density.

maybe for Version 11....

Bob


Miguel wrote:

Inbal wrote:

 As I understand from former messages posted to this list, the "load
pmesh"
command is not available in Jmol.

That is correct.

I would like to add to Prof. Henry Rezepa
request to allow such a possibility, as our
projects, currently with Chime,
are based on this option.  We used this feature
in Chime in our Molecular
symmetry Website at http://telem.openu.ac.il/symmetry.
Following the Website of Prof. Johnston  at
http://www.otterbein.edu/home/fac/dnhjhns/symmetry/symmetry.html,
we created a symmetry toolkit, based on Microsoft Excel
that automates the creation of tmesh files for the purpose
of displaying symmetry elements for various molecules.

Q: What is the difference between 'pmesh' and 'tmesh' ?

Googling on those term turned up little more than Prof. Johnston's page
mentioned above.

The project we are currently working on will allow users to
calculate the continuous symmetry measure of molecules,
thereby estimating
the distortion of molecules from a particular point group
or shape. If loading pmesh files to Jmol will be possible,
we could build this Website using Jmol.
Else - we are back to our old friend Chime.

Q: What is your timeframe for development/deployment of this website?

This item is on the Jmol task list. I hope to implement it within the next
4 to 6 months.

If you were in a position to help fund the development of this feature
then the priority could/would be raised.

Another feature that we use is the ability to load a
molecule from the user's hard disk using JavaScript.

I do not think that you are reading the files using *JavaScript*. Rather,
I assume you are reading the files through the Chime plug-in.

Reading the help files of Jmol, it was
not clear to us whether this possibility is
available in Jmol.  What is
the current status of this command?

An 'unsigned/untrusted' applet cannot read from the local file system.
That would be a security violation.

Several people have requested a 'signed' Jmol applet that would allow
access to the local file system. This would allow:
 - access to the local hard drive
 - CD-ROM distribution of browser-based applications
 - access to secondary web servers ... for example, loading
   files directly from the PDB.

In addition to the direct engineering resources required to implement and
test this, there will be a direct external cost; doing a signed Jmol
applet correctly will involve buying a code signing certificate from a
recognized certifying authority.

Again, if you were in a position to help fund some of this development it
would be greatly appreciated.


Miguel

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--

Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein

Re: [Jmol-developers] Load pmesh and load file in Jmol

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