Hello, James Precisely! PDB format has no place for atom labels or annotations, that why Jmol cannot save that. You can save to a "JMOL" file which is a file (actually a gzipped set of files) that holds everything. Of course, that file can only be opened by Jmol, You can also save to a special png file (called PNGJ) that includes a snapshot of the model and will be loaded as an image by external software but as a full model by Jmol.
I don't know of any file format that can hold annotations for each atom. Several allow comments. Maybe the newer MOL3000 has a place, but I never read about it. > This opens up what is perhaps a more general question. I don't think > JMol always supports all of the possible data fields for the file > formats it can use. Is there documentation about which features > should be assumed to work (I'm particularly thinking of when using > "write CD|MOL|PDB|SDF|V2000|XYZ|XYZRN|XYZVIB " Not exhaustive, but for several formats and features there is some documentation in the Wiki, see http://wiki.jmol.org/index.php/File_formats and there Coordinates Support for bond orders Support for isotopes Support for stereochemistry As for export, it's msotly just the atom properties that are written to file (ccordinates, identities...). ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
