Hi Angel, Thanks for the info. With respect to this: > > Assuming that none of the molecular model formats support saving > > either general visible annotations or atom labels, and that the > > solution is to write an SPT, JMOL or PNGJ, as Rob suggested, that > > would be perfect if JMol was the only program other users needed. But, > > the actual modeling may have been done in GROMACS, HyperChem, VMD, > > etc. So, the problem is round-tripping. > > And what would GROMACS, HyperChem or VMD do with that data?
That's a very good question. I suspect the answer is "nothing," which obviously moots my question. I guess what I was hoping was that there was some file format that had annotations and was standard. From what I know of HyperChem I think that JMol's annotation features are actually fairly superior, which also unfortunately means that there may be no way to make them compatible. > > probably do many other things) and give it back them as a .pdb, or > > anything that they can use without losing my changes. E.g., .spt, > > .jmol and .pngj do not appear to be on HyperChem's "open" or "save as" > list. > > Certainly not. Not are Hyperchem's proprietary files formats read by other > software, or am I wrong? Ah, maybe Jmol does read them ;-) LOL. Yeah, I think one of my misconceptions when getting into this was that, e.g., HyperChem is $1000+, it must do all the things Jmol does, not to mention all sorts of other wonderful things. Which, in fairness, it does, but not for my purposes. > So, what is your purpose? To open a pdb file in Jmol, add some labels, and be > able to keep them... Keep the original pdb for passing it along to other > software, and keep the state file for recovering the annotations when you go > back to Jmol. --maybe Not just keep them, but allow others to read and edit them in their software of choice. It's sounding like this isn't going to happen. Thanks! James ------------------------------------------------------------------------------ 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
