easy enough. Yes, carbohydrates are a bit of a pain. Adding [ALL] is no
problem.
On Sat, Apr 20, 2013 at 3:09 PM, Eric Martz <[email protected]>wrote:
> Dear Angel, Bob, and others concerned with the definition of
> carbohydrate in Jmol:
>
> Apparently Jmol defines 'carbohydrate' as a list of carbohydrate
> residues that occur in the PDB:
>
> http://wiki.jmol.org/index.php/AtomSets/Carbohydrate
>
> Earlier I constructed my own such list for use within FirstGlance,
> but since the Jmol 12 list given in the above-cited page is longer, I
> have retired my list and I will trust Jmol to know what 'carbohydrate' is.
>
> A single PDB entry, 1rpj, includes allopyranose/allose, with the ID
> [ALL]. When last I tried using this, it caused my scripts to die.
>
> I notice that it is not included in the list given in the wiki page
> cited above. Presumably it should be included. I notice that [ALL]
> now selects it, but 'carbohydrate' does not.
>
> Probably the Jmol defininition list needs to be updated in general,
> but 1rpj was deposited and released in 1999.
>
> Eric
>
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://Martz.MolviZ.Org
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--
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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