On Dec 13 2004, Simon Tyrrell wrote:
Miguel wrote:
>
>In fact, it *is* loading.
>
>There are 4 <molecule> structures in the '_symm' file. So, 4 different
>AtomSets are being created.
> >
>By default, model 1 is shown.
>
> Unfortunately, in this case model1 has no atoms ... it is only a > container for the other models.
> >
Yup this is the case. There are essentially three types of CML molecule files:
<molecule> <atomArray> ..... </atomArray> <bondArray> ..... </bondArray> </molecule>
which is a single structure. This loads up correctly in Jmol with no problems.
The second is
<molecule> <atomArray> ..... </atomArray> <bondArray> ..... </bondArray> </molecule> <molecule> <atomArray> ..... </atomArray> <bondArray> ..... </bondArray> </molecule> ....
which is a list of molecules (i.e. they could be different frames of an animation). this one doesn't appear to load correctly in the latest Jmol. I get an IllegalSaxParseException on the example list.cml file attached to this email.
There has to be only one top level element so it is normally something like:
<list>
<molecule> <atomArray> ..... </atomArray> <bondArray> ..... </bondArray> </molecule> <molecule> <atomArray> ..... </atomArray> <bondArray> ..... </bondArray> </molecule> .... </list>
which will at least parse.
We are looking at the idea of using RDF to annotate these types of input rather than hardcoding them
P.
Where there is a list of molecules it is up to Jmol what it wants to do. e.g. they might be put in a ComboBox. For a nested molecule it may be useful to show the molecules all in the same frame but to be able to switch them on and off.
The third type is when a molecule consists of separate substructures that aren't joined (i.e. disjoint). My previous email showed this type of example.
> Q: Is it the case that <molecule> substructures should all be put into > the same AtomSet/model/frame ?
>
> >
Yes. As far as Jmol is concerned does the separate substructures have to all be in the same AtomSetCollection, or is it 1 AtomSetCollection per substructure?
Imagine a protein and a ligand. This is a parent molecule with two children, probably with the same reference frame. It can be useful to display them together, but also hide one or the other. Of course Jmol has different means of selection but this alows the author to structure the info. It's most useful for crystal structures
P.
Cheers
Billy
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