Re: [Jmol-users] JmolApplet Wish List

[Miguel <mt...@mt...>]

> Miguel wrote:
> [Praise for JMol's bonding algorithm, and a request for
> molecules not rendered properly]

I apologize ... I certainly didn't mean to come across as 'praising' the
Jmol bonding algorithm.

I tried to make clear that the bonding criteria are taken from OpenBabel.

The 'praise' I gave it was that it was 'pretty fast' ... I'll accept full
responsibility for that.

> It is a while ago, and I am no longer working on that project,
> but you might remember me asking something similar in 2000.

I only started working on Jmol code in 2003.

> Out of sentimentality, I'm still lurking. I used an old version
> of the JMol Applet in a Java application I developed, and tried
> to make you aware of the fact that sometimes people calculate
> their own structures, complete with "final" bond and atom position
> information, and don't want a viewer program trying to be smart
> and decide where atoms and bonds should be.

Certainly I agree 100%.

What I believe I said in my email was:
 - we use the connectivity in .mol files
 - we *need* to use the CONECT records in .pdb files


> Did I ever report back when I finished my project? You can see
> the results at "http://www.mathematik.uni-bielefeld.de/~CaGe/".
> On the website, we praise JMol because the version we have does
> exactly what we want, but I don't know if that would still be
> true in the current version.

Your web application would certainly need some modifications to run with
the current version of Jmol.

Probably over 90% of the Jmol code has been rewritten this year ... 100%
of the applet code.

In the course of this we have explicitly dropped some functionality from
previous versions (like rendering styles).

> My point is, I didn't get all I wanted from a standard version
> of the JMol Applet, so I ended up changing bits of the source
> code myself, using CML data with a new "Convention" of "MathGraph". I
> sent messages about my changes, but these seemed to get lost
> in the activies of JMol development.
As I said, I only started working on the project this year.
If I missed a message of yours, then I apologize.

I assure you, I *want* end-user feedback.

> It would be good if a
> position such as mine wasn't completely forgotten. From that
> perspective, Miguel's response is not to the point.

I am truly sorry if my response came across as 'arrogant' or not to the
point.


> My specific requirements were:
> * Exact representation of input data in terms of atom positions
>    and bonds (Sometimes our bonds even were "impossible" from a
>    chemistry point of view, but I still wanted JMol to faithfully show
> what it was given to show.)
I agree 100%

> I also needed this to be
>    possible in CML, since that was the only format one could hand to
> the applet in a parameter. There was no scripting back then.


> * getter and setter methods for display settings (things like
>    the drawing modes that existed back then)

It isn't clear to me exactly what you are looking for, but I believe that
most of the this type of functionality should be available through the
scripting language today.

> I dreamed of being able to always take the newest version and
> "plug it in" to my application, and I'd wonder if that could be
> made possible.
>
> Sebastian Lisken

Sounds like you may have had some negative experiences with Jmol in the past.

There will be a major code base change with the upcoming v10 release.
Stability seems important to you. Therefore, I suggest you wait for the
Jmol v10 release and reevaluate it when it comes out. It it doesn't meet
your needs, then please let us know and we will add your requirements to
the list.


Miguel