Re: [COOT] Conflicting opinions on what constitutes an alpha1-6 L-fucose between Coot and Privateer
I see. Thanks, Paul, for the explanation. Of course you are right, and I see that too despite having the correct ALPHA1-6: find_glycosidic_linkage_type() for A 911 NAG,A 913 FUC returns "BETA1-6" This settles it for me. (I am not sure how Markus got beta-fucoses built by Coot the in the first place, though.) Engin On 4/23/24 8:03 PM, Paul Emsley wrote: We are talking about different things, I think. Coot's glyco builder builds alpha 1-6 linked FUC correctly. Coot's glyco validator used to (until this evening) identify the alpha 1-6 linked FUC as a beta anomer (it no longer does). See for example the G8 FUC in 8q5u: Coot 0.9.8.94 now prints: ASN [spec: 1 "A" 297 ""] pyr-ASN NAG [spec: 1 "G" 1 ""] BETA1-4 NAG [spec: 1 "G" 2 ""] BETA1-4 BMA [spec: 1 "G" 3 ""] ALPHA1-3 MAN [spec: 1 "G" 4 ""] BETA1-2 NAG [spec: 1 "G" 5 ""] BETA1-6 MAN [spec: 1 "G" 6 ""] BETA1-2 NAG [spec: 1 "G" 7 ""] ALPHA1-6 FUC [spec: 1 "G" 8 ""] Paul. On 24/04/2024 01:38, Engin Özkan wrote: CAUTION: This email originated from outside of the LMB: .-owner-c...@jiscmail.ac.uk-. Do not click links or open attachments unless you recognize the sender and know the content is safe. If you think this is a phishing email, please forward it to phish...@mrc-lmb.cam.ac.uk -- 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=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 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 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
Re: [COOT] Conflicting opinions on what constitutes an alpha1-6 L-fucose between Coot and Privateer
We are talking about different things, I think. Coot's glyco builder builds alpha 1-6 linked FUC correctly. Coot's glyco validator used to (until this evening) identify the alpha 1-6 linked FUC as a beta anomer (it no longer does). See for example the G8 FUC in 8q5u: Coot 0.9.8.94 now prints: ASN [spec: 1 "A" 297 ""] pyr-ASN NAG [spec: 1 "G" 1 ""] BETA1-4 NAG [spec: 1 "G" 2 ""] BETA1-4 BMA [spec: 1 "G" 3 ""] ALPHA1-3 MAN [spec: 1 "G" 4 ""] BETA1-2 NAG [spec: 1 "G" 5 ""] BETA1-6 MAN [spec: 1 "G" 6 ""] BETA1-2 NAG [spec: 1 "G" 7 ""] ALPHA1-6 FUC [spec: 1 "G" 8 ""] Paul. On 24/04/2024 01:38, Engin Özkan wrote: CAUTION: This email originated from outside of the LMB: .-owner-c...@jiscmail.ac.uk-. Do not click links or open attachments unless you recognize the sender and know the content is safe. If you think this is a phishing email, please forward it to phish...@mrc-lmb.cam.ac.uk -- 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=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 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 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
Re: [COOT] Conflicting opinions on what constitutes an alpha1-6 L-fucose between Coot and Privateer
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=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 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 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
[COOT] Release 0.9.8.94
It's been a few months since the last bug release of the 0.9.x. series. Here's an update so the fixes are available for CCP4 builds. o CHANGE: Add a more informative message on failure to generate rtop in transform-map-using-lsq-matrix [Martin Maly] o CHANGE: The pyranose link restraints logic has changed - hopefully more accurate now [Andrey Lebedev] o BUG-FIX: the logic of the glyco-tree glyco chiral test for ALPHA1-6 and BETA1-6 has been reversed (i.e. corrected) [who validates the validators? Markus Meier does] Source: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.94.tar.gz To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] Release 1.1.08
Not many user-visible changes in this one. o FEATURE: Scene Presets added to the Draw menu o CHANGE: "Mutate" is now a button so that it can now be used to mutate RNA and DNA. o BUG-FIX: mutate_by_overlap() fixed [thanks Simon Vecchioni] o BUG-FIX: The "Generic Display Objects" dialog now dynamically updates (no need to close it an open it again to see new generic display objects). o BUG-FIX: Undisplaying a model while the Display Manager dialog is not displayed now correctly sets the state of the Display checkbutton. Source: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.08.tar.gz To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
