Re: [Jmol-developers] CIF with lone disordered atom produces two JmolMolecule instances?

[N D. B. <hu...@gm...>]

Ok thanks Bob.

Here are some final questions to determine a consistent approach to
analysing molecules input as a unique atom set regardless of the source
data format.

If the answer to each is "yes" then I'm good to go.

Hopefully this'll be useful to others trying to use the viewer molecules
from Java.

   1.

   Is it true that every input data file regardless of format will create
   just one set of JmolNode instances?
    2.

   ..so every JmolMolecule present in JmolMolecule[] mols =
   viewer.getModelSet().getMolecules() will always reference the same
JmolNode[]
   nodes?
    3.

   ..and JmolMolecule#firstAtomIndex indicates the first atom in
   JmolMolecule#nodes, and the end index (one beyond last atom) is either
   (i) determined by same property of the next member of mols or (ii) if no
   next member exists all remaining atoms are included in the current molecule?

   I tried using the JmolMolecule#atomCount property but it seems to often
   be zero.Dave



On 17 April 2013 14:12, Robert Hanson <ha...@st...> wrote:

> Whatever program is creating this CIF file is not indicating the disorder
> groups:
>
> _atom_site_U_iso_or_equiv
> _atom_site_occupancy
> _atom_site_adp_type
> _atom_site_refinement_flags_posn
> _atom_site_refinement_flags_adp
> _atom_site_refinement_flags_occupancy
> _atom_site_disorder_assembly
> _atom_site_disorder_group
> _oxford_atom_site_special_shape
> _atom_site_attached_hydrogens
> C1 C 0.6957 0.3134 0.8670 0.0013 1.0000 Uiso . . . . . . .
> Cl2 Cl 0.7167 0.3649 1.0081 0.0252 1.0000 Uiso . . . . . . .
>
> (all those dots after Uiso; some of those should show disorder groups)
>
>
>
>
> On Tue, Apr 16, 2013 at 11:34 PM, N David Brown <hu...@gm...> wrote:
>
>>  Absolutely, see attached. In particular *solution.cif* which generates
>> 12 molecules.
>>
>> Possibly it's something I'm doing wrong but afaik I'm just running load
>> "path/to/my.cif".
>>
>> Dave
>>
>>
>> On 16 April 2013 23:27, Robert Hanson <ha...@st...> wrote:
>>
>>> Can you send me the CIF file so I can see what's happening with it?
>>>
>>>
>>> On Tue, Apr 16, 2013 at 10:18 AM, N David Brown <hu...@gm...>wrote:
>>>
>>>> When I load a CIF with a single substitutional disorder atom there are
>>>> two JmolMolecule instances in the Viewer:
>>>>
>>>> JmolMolecule[] mols = viewer.getModelSet().getMolecules(); // mols.length == 2
>>>>
>>>> I've printed out their structural info and they're identical, including
>>>> atom labels.
>>>>
>>>> Bob - you mentioned in another thread the load xxx.cif filter "%A"command. I've searched on the interactive script doc page though info is
>>>> hard to penetrate. I understand this will specify the "altLoc" atom group?
>>>>
>>>> The thing is, I need to identify and remove those JmolMolecule
>>>> instances which are equivalent.to one-another and leave just one. I
>>>> want simply the atom set that's described in the CIF, not two entire
>>>> disorder equivalent molecules that are generated.
>>>>
>>>> What's the best approach for this? Will the filter command do what's
>>>> intended?
>>>>
>>>> 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
>
>