Re: [Jmol-users] saving annotations and labels

[James R. <ja...@ry...>]

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