At 13:09 02/06/2004 +0200, Miguel wrote:
>>opacity is something that scares me. > > You mean the technical implementation? Would you settle for > visibility="on/off"?
If it is just on/off then the basic functionality is already built into jmol.
When I first read it I was thinking of transparency/translucency ... like an alpha channel.
So was I! It's what we use in SVG/2D. But I wanted to be less scary. I would guess that transparency/translucency is something that people will be asking for at some stage. But I appreciate it is a lot of effort. I assume it's easier in 2D where there is a painter's model and an object is convoluted with the pixels that remain visible
>>Q: What would be the purpose of having general graphical shapes as part >> of >>a reaction? > > It isn't just reactions - we might have things like molecular surfaces, > spheres representing the QM region, etc.. But again this isn't high > priority
OK
>>Q: what is a 'curly arrow' ? > > A paper-device for representing the movement of electrons. With animation > the movement can be explicit shown - this is a major benefit.
OK
It is possibly valuable to have bonds swing between atoms rather like gates in a field:
A B | C
changes to A-B
C
in SVG we can interpolate so we have intermediates like A B \ C
where the bond is halfway between B and C.
But an alternative is to have BC fade out and AB increase in intensity.
>>However, there is currently no mechanism to specify these attributes as >>part of the file format. That is, within the molecular model file there >> is >>no way to specify atom attributes like color or size. I do not think it >>would be difficult to do, but there is something about it that makes me >>uncomfortable. I will need to think about that. > > I agree. I think the models and their presentation should be completely > separate. So that various styles could be applied to certain molecules and > different ones to others.
OK
But, is it the case that you want all this information coming out of the same .cml file?
It's a wider issue for Jmol and related to XML/CSS stylesheets. It may be value for a user to define their own style for Jmol style and to apply it on style-free content. I would certainly separate these in some way in the CML file - in fact at present style is deliberately not part of CML unlike some other molecular formats (mainly 2D).
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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