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 MAN.cif) are
identical to current CCP4 8.0.018 version of the library (installed by CCP4
Update Manager) as well as version ccp4-8.0.018 and version ccp4-8.0.016 on
GitHub (https://github.com/MonomerLibrary/monomers)
MD5 checksums on these files are
9cfba4ac24f056d648df8227316f788b monomers/f/FUC.cif
958ac5b19a92ceec604d233457944b2a monomers/n/NAG.cif
697dd5242334dd99dad9ce43133c6382 monomers/b/BMA.cif
9d68ff54296ef2f4622005efb4eb080b monomers/m/MAN.cif
If they are different on your machine, please let me know.
I will switch monomer libraries anyway and do some testing.
I also was switching back and forth between my locally compiled coot (0.9.8.92)
and the the CCP4 distributed version (0.9.8.93 EL). I will check if there is a
difference between the two.
Thank you very much for your suggestion!
With best regards,
Markus
On 2024-04-18 13:48, Engin Özkan wrote:
Caution! This message was sent from outside the University of Manitoba.
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.
I also had private discussions with Garib Murshudov, who were correcting
the glycan monomer problems back in ~2011.
I could find old links to some of the discussions on bulletin board
archives:
https://phenix-online.org/pipermail/phenixbb/2011-November/017958.html
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg13968.html
I am curious if something got reverted or if you have some ancient
library definitions somewhere. But I hope this gives some ideas.
Best,
Engin
On 4/17/24 3:07 PM, Markus Meier wrote:
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 privateer and
unfortunately privateer flags the L-fucose as having the wrong
anomeric linkage - beta 1-6 :-(
Coot reports the same as being in the alpha 1-6 anomeric form.
I then manually built the opposite anomeric form which privateer
happily accepts as being alpha1-6. However, Coot reports it as beta 1-6.
In my understanding, the alpha configuration of a glycosidic linkage
should have the oxygen at the anomeric centre and the -CH3 group at
opposite faces of the sugar ring, so I have to agree with privateer on
this one.
Please check you code.
I have attached the two glycan trees and here is the output of
privateer and Coot for both. Coot and privateer versions are given at
the bottom.
Btw. Neither privateer nor refmac5 can read the mmCIF files that Coot
produces with the "Extract this Tree" functions. All the
_atom_site.label_*_id entries are empty!
N133_tree_privateer_alpha_anomer_FUC.cif:
Privateer:
Detailed validation data
PDB Sugar Q Phi Theta Detected type
Cnf Ctx Ok?
- -- -- ---
--- -- --- -
N133 NAG-A-459 0.597 63.27 2.85 beta-D-aldopyranose
4c1 28.09 (n) yes
N133 NAG-A-460 0.603 145.39 2.15 beta-D-aldopyranose
4c1 36.34 (n) yes
N133 BMA-A-461 0.550 333.80 4.39 beta-D-aldopyranose
4c1 45.25 (n) yes
N133 MAN-A-462 0.628 6.26 5.03 alpha-D-aldopyranose
4c1 46.22 (n) yes
N133 MAN-A-463 0.628 4.87 5.87 alpha-D-aldopyranose
4c1 50.37 (n) yes
N133 FUC-A-464 0.615 162.25 174.51 alpha-L-aldopyranose
1c4 31.24 (n) yes <-
Partially occupied monosaccharides, if any, are marked with an
asterisk (*)
SUMMARY:
Wrong anomer: 0
Wrong configuration: 0
Unphysical puckering amplitude: 0
In higher-energy conformations: 0
Privateer has identified 0 issues, with 0 of 6 sugars affected.
Coot output:
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 1
glyco close: 1.486 A 459 C1 to A 133 ND2
debug:: find_glycosidic_linkage_type() for A 459 NAG,A 133 ASN
returns "pyr-ASN"
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 4
glyco close: 2.397 A 459 C4 to A 460 C1
glyco close: 2.339 A 459 O4 to A 460 C2
glyco close: 2.318 A 459 O4 to A 460 O5
glyco close: 1.387 A 459 O4 to A 460 C1
debug:: find_glycosidic_linkage_type() for A 459 NAG,A 460 NAG
returns "BETA1-4"
DEBUG:: find_glycosidic
