Actually, that should work, provided your CIF file shows bond distances to
the A set. The file I use for testing only has bond information to one of
the alternatives.
You might use the load filter and then, if it comes back without bonds,
issue
connect auto
This should connect atoms based on distance ranges.
On Sun, Apr 14, 2013 at 6:49 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> CIF disorder sets are very complex and, I think, somewhat ambiguous. You
> might try a load filter for alternative A:
>
> load xxx.cif filter "%A"
>
> ah, but that does not work. OK there must be a bug there. I will look into
> it.
>
>
>
>
> On Sun, Apr 14, 2013 at 3:31 AM, N David Brown <hubd...@gmail.com> wrote:
>
>> I've got a CIF with substitutional disorder.
>>
>> The alternative atom A' for the disorder site is loaded by Jmol into the
>> same JmolMolecule instance as the rest of the structure. However, A' has no
>> bonds to the rest of the molecule.
>>
>> I need to split out A' into its own JmolMolecule so it's guaranteed that
>> each JmolMolecule in the viewer is a connected graph (there's an edge path
>> from every vertex in the molecule to every other).
>>
>> Is there a neat way to achieve this? I'm hoping to avoid re-importing as
>> e.g. a generated MOL string since this will use useful CIF information like
>> the unit cell parameters.
>>
>> Cheers,
>>
>> Dave
>>
>>
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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
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analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
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