Ah, OK, I see the problem. Yes, there are several of those that have
changed. NAM is not listed as obsolete because it has been replace. (WHY
would they do that??) If you feel strongly that it should be removed, I'll
go along with that. I guess it's only in one structure anyway now. But it
did used to NAM. ASF can go. I've added AMU, which is the new name for NAM
and also NDG, which is the beta form of NAG and appears in 400+ entries.
I wonder how hard it would be to get the whole list of carbohydrates from
PDB. I guess that could be a long list....
On Thu, Jun 30, 2011 at 12:29 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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
>
--
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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