Dear all, this is some kind of feature addon for the Jmol filters:
The ADF filter obviously assumes all element symbols to be simple strings. This is not always true following the ADF user guide https://www.scm.com/doc.2016/ADF/Input/Atomic_coordinates.html?highlight=atoms were "atom types" are *************************** AtomType The name of an atom type. It must begin with the standard one- or two-character symbol for the chemical element (e.g. H, He, Li,...). Optionally it may be appended by .text, where text is any string (not containing delimiters). Examples: H, Mn.3, Cu.dz-new. *************************** This feature is for example used in NMR coupling calculations when re-defining special basis sets for some of the coupling atoms. At the moment, the jmol parser apparently simply ignores atoms with names such as "H.b" so they are just lacking in the final structure. I suggest the following one line fix: ADFReader.java starting from line 159: while (rd() != null && !line.startsWith(" -----")) { tokens = getTokens(); if (tokens.length < 5) break; String symbol = tokens[1]; /* +++++++++++++ADD THIS++++++++++++++ */ if(symbol.contains(".")) { symbol = symbol.split("\\.")[0]; } /* +++++++++++++ADD THIS++++++++++++++ */ if (JmolAdapter.getElementNumber(symbol) < 1) nXX++; else addAtomXYZSymName(tokens, pt0, symbol, null); } This will just split off the things after the period and proceed with the element symbol as usual and works for me on my local files with "H.b" atoms. best Georg -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PD Dr. Georg Eickerling Universität Augsburg Institut für Physik Lehrstuhl für Chemische Physik und Materialwissenschaften ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
