I returned NAM and ASF for 12.1 -- I suggest they be returned for 12.0 as
well.
NAM is *N*-acetylmuramic
acid<http://en.wikipedia.org/wiki/N-Acetylmuramic_acid>
ASF is N-GLYCOSYL CHAIN
Was there some reason you were considering these not to be carbohydrates,
Angel? The reason to include them is that "carbohydrates" is used in its
more inclusive term, not just for Cx(H2O)y. Right?
Bob
2011/6/29 Angel Herráez <angel.herr...@uah.es>
> Dear developers,
>
> I have committed code that updates the definition of the 'carbohydrate'
> atom set. This is
> based on a list of residue IDs (provided by Eric some time ago).
>
> While working with some glycans in glycoproteins, I have found out a few
> common residues
> (N-acetyl-galactosamine and sialic acid) that were not included in the set,
> so I have added
> them in the list.
>
> While doing that, I reviewed the whole list against the PDB "Ligand Expo"
> site, http://ligand-
> expo.rcsb.org/ld-search.html and found out
> - that some listed residue IDs are now deprecated from the PDB. I have
> still left them in the
> list but have separated them and included a comment (in case we want to
> remove them in
> future)
> - that two listed residue IDs were not carbohydrates (maybe a typo), so I
> have removed them
>
> The list will now be documented at http://wiki.jmol.org/index.php/AtomSets
>
>
> Now my question:
> I'd like to introduce this change too in the 12.0.x series. Do you think it
> qualifies as a bug fix
> and so it can go there, or is it a change in behaviour and it should only
> go in the 12.1.x?
>
> Thanks for your views
> Angel
>
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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