On Tuesday 10 June 2003 20:51, Peter Murray-Rust wrote:
> Jmol can be very useful in reading multiple molecules from a single file,
> especially using CML. There seem to be two modes, both with the structure:
> <list>
> <molecule>...</molecule>
> <molecule>...</molecule>
> </list>
>
> A. when <list> has no Jmol-specific attributes all molecules are read an
> superimposed (how is this done? I assume translated to the common centre of
> mass but without rotation).
Interesting behaviour... the CMLReader simply ignores elements that it does
not parse... it, apperently, only parser <list> elements which indicate an
Jmol animation (JMOL-ANIMATION convention ;)...
Can you send me the CML file for testing purposes? I will fix the problem
then...
> This would be useful if the molecules were
> pre-aligned, but it isn't easy to see individual molecules. Also are bonds
> made *between* molecules?)
Considering my above analysis to be correct, the reader would then just read
the atoms and put them all in the same AtomContainer... Not sure how it super
imposes then, though....
> B <list convention="JMOL-ANIMATION">
> This is obviously useful for animations of reactions or dynamics.
> There seems to be no specific mechanism for viewing a list of molecules
> sequentially.
Yes, that should be the default effect of a list element... either it's a bug,
or I never implemented this behaviour... (I will)...
> A kludge is to add JMOL-ANIMATION and then single-step through the
> animation which works fine but does not display the identity of the
> molecule (BTW any display of CML id or title could be very valuable).
>
> If possible I would suggest:
>
> <list>...</list> read in a list of molecules and displayed the first one
> only (with ID). An additional Extras button could allow single-stepping
> through the list. There could also be a command to superpose the molecules
> into a collection. This would have to have options such as (no)rotate,
> (no)translate and possibly selection of superimposition method.
Alternatively, and this was my first idea, was to open up multiple Jmol
windows...
> As people increasingly use multiple data sets this could be a very valuable
> feature. ("Show me all the molecules in this document" - without spawning
> an applet for each)
Indeed.
> In CMLComp we are addressing the question of multiple views of the same
> molecule using an inheritance mechanism for (say) coordinates. We would be
> interested Jmol requirements
Indeed.
Egon
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