Re: [Jmol-developers] Re: JUMBOMarker and Jmol

[Dr P. Murray-R. <pm...@ca...>]

On Feb 23 2005, Ren=E9 Kanters wrote:

> On Feb 23, 2005, at 3:25 AM, Peter Murray-Rust wrote:
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> > At 09:13 22/02/2005 -0500, Ren=E9 Kanters wrote:
> >> Hi Peter,
> >
> > Yes. I was simply saying let's start with the most popular/tractable=20
> > one to give us experience rather than trying to do all.
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> Does anybody have an idea which file format is most used? Is it xyz,=20
> pdb, or some computational chemistry log file?

I think Jmol already has solutions for both of these.
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> >
> >> I am not sure whether I would be able to implement this, though.
> >> If I were the one that needs to do this (and again, that may not be=20
> >> the best person for the task), I would probably try to get=20
> >> JUMBOMarker to run properly
> >
> > yes
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> I got it to run, but the test_mopac.xml output file is different from=20
> mopac.xml, so either it is not working as it should, or the template=20
> used to generate the shipped xml file is different.
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We'll check.=20
> >
> >>  and see whether I can develop a template.xml for some of the Jmol=20
> >> supported filed formats,
> >
> > yes
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> I tried to follow what is going on with the mopac file from looking at=20
> the template for it. I am a bit discouraged by the fact that I see 20=20
> entity files and 7 xml files used for this, while gamess needs 16=20
> entity files and 2 xml files... It all looks very complicated to me,=20
> and I am starting to wonder whether I should have brought this up to=20
> begin with :-(...
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> >
> >> do the conversion and see how well Jmol's CML reader is able to=20
> >> handle it.
> >
> > yes
> >
> >> I assume that that will give a me a sense as to how feasible it is=20
> >> for me to come up with those templates.
> >
> > Seems fine. I think the main questions will be:
> > - what info other than molecules does Jmol wish to process
> > - what should Jmol do with multiple molecules (e.g. optimsation and=20
> > dynamics).
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> Maybe life is not as complicated for Jmol since/if the amount of=20
> information we are trying to capture is limited.
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> Currently most readers only read atomic positions, and possibly charges=
=20
> and vibration data. In the NWChem reader I added just a tiny bit more=20
> (to test out the AtomSetProperty part) and I started using a PATH=20
> property that the AtomSetChooser uses to logically group AtomSets for=20
> flip-book type animation purposes.
> All molecules are read as a separate AtomSet which are put in an=20
> AtomSetCollection. Each AtomSet is then associated with a 'frame' or=20
> 'model' on the display side.
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> Before going to far into this, I would really like to know what other=20
> people think about this. I am starting to get the feeling that it may=20
> make things overly complicated.
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> Ren=E9
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