We are starting to work on reading mmCIF files from PDBe, for "assemblies". This means the actual biological unit of the molecule, be it monomer, dimer, tetramer, etc -- manually checked since there are often several automatically prepared biological units in PDB
Apparently EBI has been applying some variation in which CIF dta fields are retained in the assemby CIF file So far we have managed (Proteopedia) to handle those idiosyncrasies, but I have hit some weird problem with 2LEV It has protein + DNA, several models. Jmol 14.4.1 Jan 15 fails to render the DNA at all These are my checks: load http://www.ebi.ac.uk/pdbe/entry-files/download/pdb2lev.ent // PDB file -- ok load http://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divide d/pdb/le/pdb2lev.ent.gz // PDB file (gz) -- ok load http://www.ebi.ac.uk/pdbe/entry-files/download/2lev_updated.cif // Updated mmCIF file -- ok load http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz // Assembly 1 (mmCIF; gz) -- DNA is not displayed select dna //19040 atoms selected hide all //37340 hidden atoms display all //0 hidden atoms // in all cases, no rendering of DNA ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
