Am 30.01.17 um 22:58 schrieb Jörg Saßmannshausen: > Dear all, > > I seem to have a display problem when I am trying to open cartesian (xyz) > files: quite often the P-C bond is not drawn which means the molecule looks > wrong. > If I am using Molden to view the structure it is perfectly ok. Exporting the > structure from Molden as a xyz file and opening that file in jmol causes this > problem. However, if I am exporting it as a mol or mol2 file the same > structure > is ok apart from an odd looking pyridine ring (two double bonds or three). > I usually save the coordinates as a cartesian file as most journals would like > to have the coordinates of the final geometry as cartesians. > > I am aware of the connect command so that would be a way out of it but I would > have thought that the standart P-C bonds will be drawn automatically > > Is there something I do wrong or why does jmol has this problem? > I am using Jmol-14.8.0 and one of the latests Oracle java on Debian Wheezy. > > Any suggestion? > I have no experience with 'xyz' files, but maybe the 'autobond' parameter is switched off and it could help to switch it on first:
set autobond on; load example.xyz; Regards, Rolf ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
