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 description: You
mean you get Coot to insert a FUC with the glycosidic bond going
equatorial, instead of axial, to Fucose?
This is how it works for me:
https://www.dropbox.com/scl/fi/yjbzstojjivmfpqdlz2os/Screen-Recording-2024-04-23-at-7.32.14-PM.mov?rlkey=zvvk7apd19wk61kt21qyc42l5&dl=0
I'll see what happens when I update to the new Coot version where Paul
has switched the logic.
By the way, privateer tells me I have zero errors and the correct alpha
anomer for Fucose.
Fuc913-a6-GlcNAc911-b-ASN258
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1
...
PDB Sugar Q Phi Theta Detected type
Cnf <Bfac> Ctx Ok?
---- ------------ ----- ------ ------ -------------------
--- ------ --- -----
test NAG-A-911 0.570 280.48 5.29 beta-D-aldopyranose
4c1 47.88 (n) yes
test FUC-A-913 0.535 92.53 177.32 alpha-L-aldopyranose
1c4 70.76 (n) yes
...
Wrong anomer: 0
Best,
Engin
On 4/18/24 4:35 PM, Markus Meier wrote:
> 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
>>
>> [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
>>
>
--
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu
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