Hi Rob,
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.
Well, it sounds like you are thinking very generally; once your plan is
refined further, let us know what exactly you are interested in doing. I
suspect you could write scripts that do just about anything. There will be
no general solution to these issues.
So, the problem is
round-tripping. If someone gives me a .pdb, I can't annotate it (nor
probably do many other things) and give it back them as a .pdb, or anything
that they can use without losing my changes.
Right, and they would not expect that, because the format does not support
it. The SDF file format (V2000/V3000) does allow adding customized records,
but that's the only one I know of like that.
http://c4.cabrillo.edu/404/ctfile.pdf
E.g., .spt, .jmol and .pngj do
not appear to be on HyperChem's "open" or "save as" list. Same when I just
scan down the list of file formats GROMACS uses
(http://www.gromacs.org/Documentation/File_Formats).
I'm guessing there is no simple answer, but any suggestions would be great.
You will need to write your own file conversion for round tripping. I doubt
it's possible to get annotations through the full cycle.
Unfortunately, I'm not being all that general - there actually are multiple
packages being used by various people and I was hoping to find a common file
format that would work with them all. I think the answer to this may be
"Don't annotate." Sounds like it just isn't possible without constraining
other people's choice of software since it's not an inherent feature of the
common file formats.
Thanks,
James
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