I have NOT removed the obsolete IDs. They are still there for
backwards compatibility. I just moved them all to the last line so
they are easily identified as such.
After all, we are supporting old atom and residue names like A T G C
in DNA, both 3' and 3* etc.
Unless the same IDs are now used
Don't get me wrong -- I'm totally supportive of this effort. I just got
mixed up because I didn't realize that PDB had a different name for NAM than
what biochemists all know as NAM (AMU). So that was missing. Here's an
example (probably of no more than 8 examples total) of where NAM is NAM:
!--
Bob Hanson wrote:
Don't get me wrong
I didn't. No worries.
PREHEADER HYDROLASE (O-GLYCOSYL) 06-DEC-79
I think that date is the key here. PDB has been doing a lot of
change. But on the other hand we all keep old files around in our
disks and webpages, so the conservative attitude is
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
I vote for bug-fix and inclusion in 12.0
Jonathan
On Jun 29, 2011, at 1:35 PM, Angel Herráez wrote:
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
You can do that, but we are very close to not doing any more bug fixes in
12.0. I'd like to release 12.0 in mid to late July.
On Wed, Jun 29, 2011 at 1:42 PM, Jonathan Gutow gu...@uwosh.edu wrote:
I vote for bug-fix and inclusion in 12.0
Jonathan
On Jun 29, 2011, at 1:35 PM, Angel Herráez
I mean 12.2
On Wed, Jun 29, 2011 at 4:15 PM, Robert Hanson hans...@stolaf.edu wrote:
You can do that, but we are very close to not doing any more bug fixes in
12.0. I'd like to release 12.0 in mid to late July.
On Wed, Jun 29, 2011 at 1:42 PM, Jonathan Gutow gu...@uwosh.edu wrote:
I vote
I returned NAM and ASF for 12.1 -- I suggest they be returned for 12.0 as
well.
NAM is *N*-acetylmuramic
acidhttp://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
