From: N D. B. <hu...@gm...> - 2013-04-18 08:28:05
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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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Precog is a next-generation analytics platform capable of advanced >>>> 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! >>>> http://www2.precog.com/precogplatform/slashdotnewsletter >>>> _______________________________________________ >>>> Jmol-developers mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>> >>>> >>> >>> >>> -- >>> 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 > > |