On Wed, May 8, 2013 at 8:06 AM, James Ryley <[email protected]> wrote:
> If you open a .pdb, add a label to one or more atoms, and then “write PDB
> test.pdb”, the resulting file doesn’t seem to have the annotations. I could
> be missing something, like having my default for pdb annotations being
> “off”. But, assuming that is not the case, can one save annotations and
> labels to .pdb? To any of the model formats (preferably one that can also
> save the rotations)?****
>
> **
>
Yes, that's right. PDB files do not have annotations. In fact, the write
PDB does a very generic PDB file write.
What you want to write is an SPT ("Jmol State Script") or JMOL ("Jmol zip
file format") or PNGJ ("image + zip") file.
> **
>
> 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.
>
It's as complete as we are aware; always willing to include more. Such as?
> 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 “, but if there things it would
> ignore on “load”, that would be very useful to know also), and which do not?
> ****
>
> **
>
Well, probably if we are ignoring something, we aren't aware they are
there, so that probably would not work.
Bob Hanson
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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