Daniel wrote:
> In our
> very first looks at using Jmol we saw two problems. The first is
> essentially what is described above. we needed a way to label
> pharmacophore points and have the label be displayed, even if the atom
> was dummy atom.
OK, there is now the basic infrastructure in place to support the display
of arbitrary atom properties as a 'label' associated with the atom.
> The
> second problem we saw was that Jmol tried to draw bonds between all
> atoms that were close together. Is there a way to tell it to draw only
> those bonds that are explicitly given?
This is easily controlled.
Jmol would rather *never* calculate bonds. However, we are forced to do so
for some file formats.
These are the general rules (which we can tweak as needed):
- if there are no bonds, then run autobonding
- if the file is not a .pdb file and there are any bonds present,
only use the bonds that are present
- if the file is a .pdb file, then
* if the # of bonds is less than 1/2 the number of atoms,
assume that this is a partial set of bonds and run autobonding
* else, assume that this is a full set of bonds and do not
run autobonding
>> Q: Are there file types that store arbitrary property values for
>> atoms?
>
> I'm not sure about file types, we are using CML. We do have work on a
> database that will store this type of data.
I am not that familiar with CML yet ... but we can certainly support
arbitrary properties within CML.
Not sure how we will deal with Units ... the Jmol property display support
can render a single string for a property. We can just cat on the units if
you want.
Miguel
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