Hi Paul,
I just rebuilt coot-0.9.8.94, coot-0.9.8.93 and coot-0.9.8.92 from scratch,
deleting the previous installs.
The glyco validator in version coot-0.9.8.94 is indeed fixed. Thank you so much!
Also, coot-0.9.8.93 and coot-0.9.8.92 now build an alpha1-6 fucose correctly
into the electron
Hi Engin,
thank you for all the trouble you went through to make this presentation! The
glycosidic bond in your presentation is indeed correct (alpha1-6).
Not sure how to interpret the terms axial or equatorial; I followed the
definition from here:
I see. Thanks, Paul, for the explanation. Of course you are right, and I
see that too despite having the correct ALPHA1-6:
find_glycosidic_linkage_type() for A 911 NAG,A 913 FUC returns "BETA1-6"
This settles it for me.
(I am not sure how Markus got beta-fucoses built by Coot the in the
We are talking about different things, I think.
Coot's glyco builder builds alpha 1-6 linked FUC correctly.
Coot's glyco validator used to (until this evening) identify the alpha
1-6 linked FUC as a beta anomer (it no longer does).
See for example the G8 FUC in 8q5u: Coot 0.9.8.94 now
Hi Markus,
I am using Coot that comes with CCP4 8, which has FUC (alpha-L-Fucose)
with an oxygen on C1 in the axial position. Which is the correct form, I
believe.
Using Coot 0.9.8.93, I get my alpha1-6 and alpha1-3 (insect) Fucoses
inserted correctly. I had trouble understanding your
On 17/04/2024 21:07, Markus Meier wrote:
Hi Paul,
thank you for implementing the Glyco module in Coot!
It is not in Coot 1 (yet). It needs to be rewritten.
I used its "Add N-linked Glycan" function to build an N-linked glycan
which contains L-fucose with an alpha1-6 glycosidic linkage on
Hi Engin,
hmm, it appears I was using the monomer library from
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/monomers-2023-01-02-23:57:29.tar.gz
(it gets installed automatically with Coot's build-it script).
However, the files in question (FUC.cif, NAG.cif, BMA.cif and
Hi Markus,
There were reports to the ccp4bb and phenixbb back in 2011 about
something similar. The monomer library files for FUC and/or the linkage
definitions for refmac/phenix were not right. I think. My recollection
is that this was corrected, and I could not reproduce your observation.
Hi Paul,
thank you for implementing the Glyco module in Coot!
I used its "Add N-linked Glycan" function to build an N-linked glycan which
contains L-fucose with an alpha1-6 glycosidic linkage on the first N-acetyl glucosamine
of the tree.
However, after exporting the tree, I checked it with
