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:
https://www.masterorganicchemistry.com/2018/02/19/the-big-damn-post-of-sugar-nomenclature
However, judging from the drawings here (https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Alkanes/Properties_of_Alkanes/Cycloalkanes/Rings%3A_cis_trans_and_axial_equatorial_relationships), yes, the glycosidic bond in my case is equatorial and privateer reports it as beta1-6.
Its not urgent at all, but if you find a moment, could you please send me the terminal output of Coot it reports regarding your glycosidic linkages? To do that, start Coot from a terminal and load your carbohydrate tree. Centre on one of the atoms in your carbohydrate tree, open the "Add N-linked Glycan" panel in the Glyco module and press "Update for Current Residue". Coot will print debug info on the terminal.
In the unlike case that terminal output is disabled, you can enable it in Edit->Preferences->Other->Console->Display state commands in console?->Yes
Could you also send me the coordinates of your carbohydrate tree? It would like to load it in my Coot version(s) and check the terminal output.
Thanks again!
With best regards,
Markus
On 2024-04-23 19:38, Engin Özkan wrote:
> Caution! This message was sent from outside the University of Manitoba.
>
>
> 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
--
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: [log in to unmask]
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