Ok I’ve figured it out now - looks these steps will work to load a custom
format into the viewer, as long as atomic coordinates don’t matter to you:
- Use load data as an intermediary format to load my custom .graph file.
- Apply a random position for each atom defined in the data model, and
record each position.
- Apply labels by selecting atom at each recorded position then applying
known label.
- Delete all predicted bonds and add bonds from .graph file.
On 14 September 2014 13:22, N David Brown <[email protected]> wrote:
> Thanks Angel, I’m looking into load data now actually.
>
> The positions don’t matter for my purposes, I just need to create
> JmolMolecule data types so some existing code I have can operate on this
> custom format in the same manner it operates on other formats.
>
> On 14 September 2014 13:31, Angel Herráez <[email protected]> wrote:
>
> Dave, if you do not have coordinates, how would you expect Jmol to position
>> the atoms?
>> Note that when Jmol reads Smiles, I think it does not build the molecule,
>> but
>> goes to a server that will provide it with 3D coords.
>>
>> I think that instead of loading a model file with your format, you might
>> achive
>> it using script and maybe the data command to **build** the molecule
>> inside
>> Jmol. But the question about what coordinates to use is there.
>>
>>
>>
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>
>
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