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
[log in to unmask]" target="_blank">https:[log in to unmask]
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 <Bfac> 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_linkage_type() number of sorted distances: 3
> #### glyco close: 2.347 A 460 O4 to A 461 C2
> #### glyco close: 2.346 A 460 O4 to A 461 O5
> #### glyco close: 1.398 A 460 O4 to A 461 C1
> debug:: find_glycosidic_linkage_type() for A 460 NAG,A 461 BMA
> returns "BETA1-4"
> DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 1
> #### glyco close: 1.407 A 461 O6 to A 462 C1
> debug:: find_glycosidic_linkage_type() for A 461 BMA,A 462 MAN
> returns "ALPHA1-6"
> DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 1
> #### glyco close: 1.403 A 461 O3 to A 463 C1
> debug:: find_glycosidic_linkage_type() for A 461 BMA,A 463 MAN
> returns "ALPHA1-3"
> DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 2
> #### glyco close: 2.385 A 459 O6 to A 464 O5
> #### glyco close: 1.399 A 459 O6 to A 464 C1
> debug:: find_glycosidic_linkage_type() for A 459 NAG,A 464 FUC
> returns "BETA1-6" <-
>
> ##########################################################################################
>
> N133_tree_privateer_beta_anomer_FUC.cif:
>
> Privateer:
> Detailed validation data
> ------------------------
>
> PDB Sugar Q Phi Theta Detected type
> Cnf <Bfac> Ctx Ok?
> ---- ------------ ----- ------ ------ -------------------
> --- ------ --- -----
> N133 NAG-A-459 0.539 93.90 14.28 beta-D-aldopyranose
> 4c1 17.31 (n) yes
> N133 NAG-A-460 0.576 3.57 3.48 beta-D-aldopyranose
> 4c1 28.29 (n) yes
> N133 BMA-A-461 0.534 312.39 9.79 beta-D-aldopyranose
> 4c1 42.24 (n) yes
> N133 MAN-A-462 0.580 219.67 4.19 alpha-D-aldopyranose
> 4c1 42.02 (n) yes
> N133 MAN-A-463 0.563 294.23 4.86 alpha-D-aldopyranose
> 4c1 47.39 (n) yes
> N133 FUC-A-464 0.542 120.60 172.19 beta-L-aldopyranose
> 1c4 18.87 (n) no <-
>
> Partially occupied monosaccharides, if any, are marked with an
> asterisk (*)
>
> SUMMARY:
>
> Wrong anomer: 1
> Wrong configuration: 0
> Unphysical puckering amplitude: 0
> In higher-energy conformations: 0
>
> Privateer has identified 1 issues, with 1 of 6 sugars affected.
>
> Coot:
> DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 1
> #### glyco close: 1.462 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: 2.355 A 459 C4 to A 460 C1
> #### glyco close: 2.316 A 459 O4 to A 460 O5
> #### glyco close: 2.313 A 459 O4 to A 460 C2
> #### 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_linkage_type() number of sorted distances: 3
> #### glyco close: 2.37 A 460 O4 to A 461 C2
> #### glyco close: 2.344 A 460 O4 to A 461 O5
> #### glyco close: 1.401 A 460 O4 to A 461 C1
> debug:: find_glycosidic_linkage_type() for A 460 NAG,A 461 BMA
> returns "BETA1-4"
> DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 1
> #### glyco close: 1.408 A 461 O6 to A 462 C1
> debug:: find_glycosidic_linkage_type() for A 461 BMA,A 462 MAN
> returns "ALPHA1-6"
> DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 3
> #### glyco close: 2.39 A 461 C3 to A 463 C1
> #### glyco close: 2.389 A 461 O3 to A 463 C2
> #### glyco close: 1.398 A 461 O3 to A 463 C1
> debug:: find_glycosidic_linkage_type() for A 461 BMA,A 463 MAN
> returns "ALPHA1-3"
> DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 1
> #### glyco close: 1.414 A 459 O6 to A 464 C1
> debug:: find_glycosidic_linkage_type() for A 459 NAG,A 464 FUC
> returns "ALPHA1-6" <-
>
> Program versions:
> Coot 0.9.8.93 EL (ccp4) on Gentoo Linux 64 bit
> Privateer version MKIV : 06/02/2 CCP4 8.0.019 on Gentoo Linux 64 bit
>
> With best regards,
> Markus
>
--
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
http://ozkan.uchicago.edu
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