Re: [COOT] real space refinement of alpha-23 link between GAl and Sia fails
On 22/11/2023 14:02, Keitaro Yamashita wrote: CAUTION: This email originated from outside of the LMB. Do not click links or open attachments unless you recognize the sender and know the content is safe. .-owner-c...@jiscmail.ac.uk-. Great, you are using the very latest CCP4 (with the latest monomer library). I suppose Refmac properly identified the "ALPHA2-3" link which should also appear in the PDB header (LINKR). Using Coot, I just tried PDB 2osx which includes the ALPHA2-3 link between GAL (B/2) and SIA (B/3). As you mentioned, it didn't work. debug:: find_glycosidic_linkage_type() for B 3 SIA,B 2 GAL returns "ALPHA2-3" DEBUG:: make_other_types_of_link() "ALPHA2-3" for [spec: model 1 "B"3 "" " C1 " ""] [spec: model 1 "B" 2 "" " C3 " ""] detected DEBUG:: make_other_types_of_link(): now making a link restraint [spec: 1 "B" 3 ""] [spec: 1 "B" 2 ""] with type ALPHA2-3 and order switch 0 DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0 debug:: find_glycosidic_linkage_type() for B 3 SIA,B 1 BGC returns "" DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0 debug:: find_glycosidic_linkage_type() for B 1 BGC,B 3 SIA returns "" Made 0 CHO-SS-and-other bond restraints Made 0 CHO-SS-and-other angle restraints Made 0 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints It actually found the ALPHA2-3 link (but between C1 and C3? it's strange..) and finally it didn't add any restraints. Paul, could you please look into this? Hi Keitaro, When I was looking at carbohydrate linking (quite a few years ago now), the SIA links were deliberately omitted because there was a bug (or more) in the monomer library. It seems that it is now time to revisit SIA linking. I'll add it to the list now. Regards, Paul. 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/
Re: [COOT] real space refinement of alpha-23 link between GAl and Sia fails
Hi Keitaro, thanks for confirming this. Strange that if found a link to C1? It needs to be C2, because C1 is not part of the ring. I tried with pdb-ID 6xtg and it also didn't work. Yes, refmac identified the link and lists it in the log file. Best Regards Christian On Wed, Nov 22, 2023 at 3:03 PM Keitaro Yamashita < keitaro-yamash...@g.ecc.u-tokyo.ac.jp> wrote: > Great, you are using the very latest CCP4 (with the latest monomer > library). I suppose Refmac properly identified the "ALPHA2-3" link > which should also appear in the PDB header (LINKR). > > Using Coot, I just tried PDB 2osx which includes the ALPHA2-3 link > between GAL (B/2) and SIA (B/3). As you mentioned, it didn't work. > > >debug:: find_glycosidic_linkage_type() for B 3 SIA,B 2 GAL returns > "ALPHA2-3" > > DEBUG:: make_other_types_of_link() "ALPHA2-3" for [spec: model 1 "B" > 3 "" " C1 " ""] [spec: model 1 "B"2 "" " C3 " ""] detected > > DEBUG:: make_other_types_of_link(): now making a link restraint [spec: 1 > "B" 3 ""] [spec: 1 "B" 2 ""] with type ALPHA2-3 and order switch 0 > > DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0 > >debug:: find_glycosidic_linkage_type() for B 3 SIA,B 1 BGC returns "" > > DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0 > >debug:: find_glycosidic_linkage_type() for B 1 BGC,B 3 SIA returns "" > >Made 0 CHO-SS-and-other bond restraints > >Made 0 CHO-SS-and-other angle restraints > >Made 0 CHO-SS-and-other plane restraints > >Made 0 CHO-SS-and-other trans-peptide restraints > > It actually found the ALPHA2-3 link (but between C1 and C3? it's > strange..) and finally it didn't add any restraints. Paul, could you > please look into this? > > Best regards, > Keitaro > > On Wed, 22 Nov 2023 at 19:53, Christian Roth > wrote: > > > > Ah yes, sorry forgot that crucial information. It is Coot 0.9.8.92 > Marina Bay. Installed as part of CCP4 8.0. Currently on updated 16. > > > > Best > > Christian > > > > On Wed, Nov 22, 2023 at 11:14 AM Keitaro Yamashita < > keitaro-yamash...@g.ecc.u-tokyo.ac.jp> wrote: > >> > >> Dear Christian, > >> > >> What is the version of Coot, and how did you install it? > >> > >> Best regards, > >> Keitaro > >> > >> On Wed, 22 Nov 2023 at 19:02, Christian Roth < > christianroth...@gmail.com> wrote: > >> > > >> > Hi, > >> > I have a sugar ligand with a Sia linked alpha 23 to Gal. Refinement > with Refmac of phenix works and the link is recognized from the monomer > dictionary. After opening in Coot all intersugarbonds/links are shown > properly. Realspace refinement works for the other bonds, but the Sia Gal > bond gets broken and the SIA is pushed away. The distance increases to > about 3Ang. Looks like they are treated as not connected and this is the > antibump distance? > >> > Taken into account that this is a standard link from the monomer > library I would have suspected Coot recognizes that link automatically. > What is the source for that behaviour and do I need to supply an additional > dictionary for this link? > >> > > >> > Thanks and Best > >> > Christian > >> > > >> > > >> > > >> > To unsubscribe from the COOT list, click the following link: > >> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > 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/
Re: [COOT] real space refinement of alpha-23 link between GAl and Sia fails
Great, you are using the very latest CCP4 (with the latest monomer library). I suppose Refmac properly identified the "ALPHA2-3" link which should also appear in the PDB header (LINKR). Using Coot, I just tried PDB 2osx which includes the ALPHA2-3 link between GAL (B/2) and SIA (B/3). As you mentioned, it didn't work. >debug:: find_glycosidic_linkage_type() for B 3 SIA,B 2 GAL returns > "ALPHA2-3" > DEBUG:: make_other_types_of_link() "ALPHA2-3" for [spec: model 1 "B"3 "" > " C1 " ""] [spec: model 1 "B"2 "" " C3 " ""] detected > DEBUG:: make_other_types_of_link(): now making a link restraint [spec: 1 "B" > 3 ""] [spec: 1 "B" 2 ""] with type ALPHA2-3 and order switch 0 > DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0 >debug:: find_glycosidic_linkage_type() for B 3 SIA,B 1 BGC returns "" > DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0 >debug:: find_glycosidic_linkage_type() for B 1 BGC,B 3 SIA returns "" >Made 0 CHO-SS-and-other bond restraints >Made 0 CHO-SS-and-other angle restraints >Made 0 CHO-SS-and-other plane restraints >Made 0 CHO-SS-and-other trans-peptide restraints It actually found the ALPHA2-3 link (but between C1 and C3? it's strange..) and finally it didn't add any restraints. Paul, could you please look into this? Best regards, Keitaro On Wed, 22 Nov 2023 at 19:53, Christian Roth wrote: > > Ah yes, sorry forgot that crucial information. It is Coot 0.9.8.92 Marina > Bay. Installed as part of CCP4 8.0. Currently on updated 16. > > Best > Christian > > On Wed, Nov 22, 2023 at 11:14 AM Keitaro Yamashita > wrote: >> >> Dear Christian, >> >> What is the version of Coot, and how did you install it? >> >> Best regards, >> Keitaro >> >> On Wed, 22 Nov 2023 at 19:02, Christian Roth >> wrote: >> > >> > Hi, >> > I have a sugar ligand with a Sia linked alpha 23 to Gal. Refinement with >> > Refmac of phenix works and the link is recognized from the monomer >> > dictionary. After opening in Coot all intersugarbonds/links are shown >> > properly. Realspace refinement works for the other bonds, but the Sia Gal >> > bond gets broken and the SIA is pushed away. The distance increases to >> > about 3Ang. Looks like they are treated as not connected and this is the >> > antibump distance? >> > Taken into account that this is a standard link from the monomer library I >> > would have suspected Coot recognizes that link automatically. What is the >> > source for that behaviour and do I need to supply an additional dictionary >> > for this link? >> > >> > Thanks and Best >> > Christian >> > >> > >> > >> > To unsubscribe from the COOT list, click the following link: >> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 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/
Re: [COOT] real space refinement of alpha-23 link between GAl and Sia fails
Ah yes, sorry forgot that crucial information. It is Coot 0.9.8.92 Marina Bay. Installed as part of CCP4 8.0. Currently on updated 16. Best Christian On Wed, Nov 22, 2023 at 11:14 AM Keitaro Yamashita < keitaro-yamash...@g.ecc.u-tokyo.ac.jp> wrote: > Dear Christian, > > What is the version of Coot, and how did you install it? > > Best regards, > Keitaro > > On Wed, 22 Nov 2023 at 19:02, Christian Roth > wrote: > > > > Hi, > > I have a sugar ligand with a Sia linked alpha 23 to Gal. Refinement with > Refmac of phenix works and the link is recognized from the monomer > dictionary. After opening in Coot all intersugarbonds/links are shown > properly. Realspace refinement works for the other bonds, but the Sia Gal > bond gets broken and the SIA is pushed away. The distance increases to > about 3Ang. Looks like they are treated as not connected and this is the > antibump distance? > > Taken into account that this is a standard link from the monomer library > I would have suspected Coot recognizes that link automatically. What is the > source for that behaviour and do I need to supply an additional dictionary > for this link? > > > > Thanks and Best > > Christian > > > > > > > > To unsubscribe from the COOT list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > 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/
Re: [COOT] real space refinement of alpha-23 link between GAl and Sia fails
Dear Christian, What is the version of Coot, and how did you install it? Best regards, Keitaro On Wed, 22 Nov 2023 at 19:02, Christian Roth wrote: > > Hi, > I have a sugar ligand with a Sia linked alpha 23 to Gal. Refinement with > Refmac of phenix works and the link is recognized from the monomer > dictionary. After opening in Coot all intersugarbonds/links are shown > properly. Realspace refinement works for the other bonds, but the Sia Gal > bond gets broken and the SIA is pushed away. The distance increases to about > 3Ang. Looks like they are treated as not connected and this is the antibump > distance? > Taken into account that this is a standard link from the monomer library I > would have suspected Coot recognizes that link automatically. What is the > source for that behaviour and do I need to supply an additional dictionary > for this link? > > Thanks and Best > Christian > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 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/
