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
--
Markus Meier, Ph.D.
Research Associate
University of Manitoba
Department of Chemistry
144 Dysart Road
Winnipeg, MB, R3T 2N2, Canada
Phone: +1 204 474 7172
E-mail: markus.me...@umanitoba.ca
########################################################################
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N133_tree_privateer_beta_anomer_FUC.cif
Description: CIF chemical test
N133_tree_privateer_alpha_anomer_FUC.cif
Description: CIF chemical test
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" <-
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