Hi Bob (and the others), thanks for your answer - this helps enormously. I have a bunch of legacy files created by a legacy utility - I modified the code to no longer put stuff after the integer.
As a side note: the xyz::broken.xyz trick also works on the command line (which is how I start jmol in most cases). Peter > On 26 Sep 2016, at 13:42, Robert Hanson <hans...@stolaf.edu> wrote: > > The xyz reader ignores everything else on the first line after the integer. > > The reader format resolver is what requires just an integer (the number of > atoms) and white space on the first line in order to send the data to the xyz > reader, because there are several other formats that start with an integer. > > So the documentation is technically not incorrect, but what it does not say > is that if you do not specify the format using "xyz::" as a prefix to the > file name in the LOAD command, then Jmol will not recognize your file as > "XYZ" format. > > So no need to change your files unless you need to drag-drop them into Jmol > or JSmol. If you are using the LOAD command, just do it like this: > > load "xyz::broken.xyz <http://broken.xyz/>" > > It would not be impossible to add one more check to Jmol's resolver to allow > for this. But that would introduce a whole new problem of "false positives," > and it probably would be better to align the documentation with what is > standard and indicated at https://en.wikipedia.org/wiki/XYZ_file_format > <https://en.wikipedia.org/wiki/XYZ_file_format> rather than allowing that > resolution. > > Bob > > > > > > On Mon, Sep 26, 2016 at 5:46 AM, Peter Brommer <p.brom...@warwick.ac.uk > <mailto:p.brom...@warwick.ac.uk>> wrote: > Hi, > > This concerns Jmol Version: 14.6.1_2016.08.11 2016-08-11 22:11. > > There is an issue with reading/recognising xyz files. On the wiki page > http://wiki.jmol.org/index.php/File_formats/Formats/XYZ > <http://wiki.jmol.org/index.php/File_formats/Formats/XYZ> those are described > as having two header lines per step in a multi-step format, the first of > which states "the number of atoms in that step. This integer may be preceded > by whitespace; anything on the line after the integer is ignored.” > > However, if there is anything after the integer, the xyz file is no longer > recognised and the load command gives up with “script ERROR: unrecognised > file format for file broken.xyz <http://broken.xyz/>". I attach two files > which only differ by a supposedly ignored character after the number of > atoms, and both fulfil the standard given in the wiki. > > So, at the moment there is a discord between documentation and code. I’d > prefer this was fixed in the code, so I don’t have to change a bunch of xyz > files. > > Cheers, > > Peter > > -- > Peter Brommer > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/jmol-users > <https://lists.sourceforge.net/lists/listinfo/jmol-users> > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr <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 > > ------------------------------------------------------------------------------ > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/jmol-users > <https://lists.sourceforge.net/lists/listinfo/jmol-users> -- Dr Peter Brommer Assistant Professor | Warwick Centre for Predictive Modelling | School of Engineering | University of Warwick pbrom...@warwick.ac.uk | www.warwick.ac.uk/pbrommer | External: +44 (0) 24 7652 8613 | Internal: 28613 D2.08 | School of Engineering | Library Road | Coventry | CV4 7AL | United Kingdom
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