On 8 May 2013 at 12:23, James Ryley wrote: > and thereby asking if I am misunderstanding something about .pdb. I guess > these generally are not visual annotations/labels as I am thinking of.
I agree. They are not associated to atoms. Some of those records, like SITE, are indeed read and used by Jmol. Also, several sites like Proteopedia and FirstGlance in Jmol do make use of part of the header fields and offer them to the user parsed into the intergace of the webpage where Jmol is embedded. For most of those records/fields, pdb is THE format. I see no reason to move them to another format. Anyway, have you tried OpenBabel? That is a converter between formats. > 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? > 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 ;-) 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 The most expandable format that I know is MOL3000. Maybe there is a solution for you in that spec. Also, PDB will hold whatever extra information you want inside HEADER records --I seem to recall that there are USER records too. But again, who is going to read them back? You could parse them if you make your own software. ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
