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

[Miguel <mi...@jm...>]

Inbal wrote:

>   As I understand from former messages posted to this list, the =22load=

> pmesh=22
> 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 nex=
t
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