Rolf, I have the intra-ligand bonding working now with the updated CIF format that Sameer sent me a link to. I think you also got that, right?
Now I have to implement _struct_conn for the inter-group links. This is somewhat more problematic, as CONECT is some sort of subset of these. I am hoping I can map them properly; obviously we don't want all possibilities. Do you have an idea which ones (metalic, covalent, etc.) ? I think the sensible way to implement this is to use load *XXXX* load =XXXX* where suffix * means "updated CIF" I think it's not clear exactly how these CIF files will be distributed. The problem for us is that Jmol states must access the exact file -- or at least know not to try to access the _chem_comp data even if it is present if the state originally read the pre-updated CIF file. That could be tricky. Bob On Mon, Aug 10, 2015 at 5:02 AM, Rolf Huehne <rhue...@fli-leibniz.de> wrote: > On 08/08/2015 06:53 PM, Robert Hanson wrote: > > I will contact RCSB and find out why they have dropped the CONECT bonding > > and also find out if our PDB links will fail. I think they will not, but > I > > will make sure. > > > I tried to find the announcement of the wwPDB about dropping the PDB > format in 2016 again but I couldn't find it in the news archive. > I am quite sure there was a longer statement on that but the only hints > I could find now are on these two pages: > > 1) http://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html > "What should every PDB user know about PDBx/mmCIF? > 1. The PDB file format will be phased out in 2016." > > 2) http://pdbj.org/help/data-format > "[PDB Format] > ...It will be phased out from 2016." > > Regards, > Rolf > -- > > Rolf Huehne > Postdoc > > Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) > Beutenbergstrasse 11 > 07745 Jena, Germany > > Phone: +49 3641 65 6205 > Fax: +49 3641 65 6210 > E-Mail: rhue...@fli-leibniz.de > Website: http://www.fli-leibniz.de > > Scientific Director: Prof. Dr. K. Lenhard Rudolph > Head of Administration: Dr. Daniele Barthel > Chairman of Board of Trustees: Dennys Klein > > VAT No: DE 153 925 464 > Register of Associations: No. 230296, Amtsgericht Jena > Tax Number: 162/141/08228 > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry 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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