I think that was the first issue Michelle had that was resolved. The second was additional links, that’s what Im referring to.
-- Kelvin Lau https://people.epfl.ch/kelvin.lau Scientist - Protein production and structure core facility – PTPSP President – ACIDE EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin....@epfl.ch<mailto:kelvin....@epfl.ch> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267> On 08.10.2024, 11:31, "Eleanor Dodson" <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote: Hmm - if the residues are numbered sequentially and the CSO is labelled in the dictionary as a peptide doesn't the peptide link get made internally in the refinement programs? Eleanor On Tue, 8 Oct 2024 at 09:20, Kelvin Lau <00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk<mailto:00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk>> wrote: I find that moving between Coot and Phenix sometimes there are issues. To refine in Phenix and for the links to hold in Coot I had to make custom links that survive both programs. An Example is below, it’s a Ligand-Cys bond, it’s a S-S bond but since its not part of a canonical amino acid its not recognized. You have to first define what the linked atoms are and then define the bond parameters. Have you tried to in phenix to make a cif-link.params file: Ie refinement.pdb_interpretation.apply_cif_link { data_link = LIG-CYS residue_selection_1 = chain X and resname LIG and resid 702 and name S15 residue_selection_2 = chain C and resname CYS and resid 434 and name SG } refinement.pdb_interpretation.apply_cif_link { data_link = LIG-CYS residue_selection_1 = chain Y and resname LIG and resid 702 and name S15 residue_selection_2 = chain A and resname CYS and resid 434 and name SG } refinement.pdb_interpretation.apply_cif_link { data_link = LIG-CYS residue_selection_1 = chain Z and resname LIG and resid 702 and name S15 residue_selection_2 = chain B and resname CYS and resid 434 and name SG } And then to definie a new type of data_link.cif that isn’t in the database? data_link_LIG-CYS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd LIG-CYS 1 S15 2 SG single 2.031 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd LIG-CYS 1 C14 1 S15 2 SG 110.000 3.000 LIG-CYS 1 S15 2 SG 2 CB 110.000 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id<http://chem_link_tor.id> _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period LIG-CYS ss 1 C14 1 S15 2 SG 2 CB 90.00 10.0 2 # -- Kelvin Lau https://people.epfl.ch/kelvin.lau Scientist - Protein production and structure core facility – PTPSP President – ACIDE EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin....@epfl.ch<mailto:kelvin....@epfl.ch> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267> On 08.10.2024, 07:54, "Mailing list for users of COOT Crystallographic Software on behalf of Michelle Miller" <COOT@JISCMAIL.AC.UK<mailto:COOT@JISCMAIL.AC.UK> on behalf of 0000eb408161463a-dmarc-requ...@jiscmail.ac.uk<mailto:0000eb408161463a-dmarc-requ...@jiscmail.ac.uk>> wrote: Thanks, Keitaro – that indeed solves my first problem! Unfortunately, the fix doesn’t seem to be quite as simple for the second problem. From: Keitaro Yamashita <keitaro-yamash...@g.ecc.u-tokyo.ac.jp<mailto:keitaro-yamash...@g.ecc.u-tokyo.ac.jp>> Date: Tuesday, 8 October 2024 at 4:03 pm To: Michelle Miller <mille...@wehi.edu.au<mailto:mille...@wehi.edu.au>> Cc: COOT@jiscmail.ac.uk<mailto:COOT@jiscmail.ac.uk> <COOT@jiscmail.ac.uk<mailto:COOT@jiscmail.ac.uk>> Subject: Re: Help with linking two amino acid side-chains Dear Michelle, CSO is a peptide in the latest monomer library, which is included in CCP4 9.0. I suppose you are using an old version. At least the first issue may be sorted by using COOT from CCP4 9.0. Best regards, Keitaro On Tue, 8 Oct 2024 at 13:30, Michelle Miller <0000eb408161463a-dmarc-requ...@jiscmail.ac.uk<mailto:0000eb408161463a-dmarc-requ...@jiscmail.ac.uk>> wrote: > > Hi, > > > > I’m trying to model a N-O-S bond between a lysine side-chain and an oxidised > cysteine (CSO) as described in > https://www.nature.com/articles/s41467-024-48109-3 > > > > I’m facing two problems in Coot (v 0.9.8.3): > > > > Firstly, when I go >Replace residue and replace the cysteine with a CSO – > Coot does not recognise the CSO as part of the peptide chain. I can manually > (roughly) put it in place and Phenix will fix it during refinement, however > this continues to be a problem for coot. > > > > Secondly, I have tried a couple of ways to model the NOS bond and none of > them seem to work correctly. > > > > I defined the link using JLigand, saved the cif file and the LINK record. I > manually put this link in place in Coot, loaded the cif file into Phenix and > it sort of worked, although the O-N bond length is too long and doesn’t match > what is defined in the cif file (~1.99 Å vs 1.38 Å). Furthermore, after > loading the cif file in coot, when I try to do a real space refine, it does > not recognise the O-N link (or the CSO as part of the peptide chain as > described above). > I defined the entire CSO-LYS as a ligand and generated cif restraints in > Phenix using elBOW, loaded the pdb into Coot and placed into the density, > merged with the pdb and tried to define “links” to the peptide backbone on > both sides. As above, these bonds are not recognised by coot. After running > through phenix, the planarity of the amide bonds is lost. > > > > To add to the complexity, there are two conformations of the N-O-S > modification/linkage, so I also want to be able to model that. > > > > Any help would be greatly appreciated!! > > > > Thanks, > > Michelle > > > > --------------------------------------- > > Michelle Miller PhD > > Senior Research Officer > > Structural Biology > > > > E mille...@wehi.edu.au<mailto:mille...@wehi.edu.au> > > > > > Walter and Eliza Hall Institute of Medical Research > 1G Royal Parade Parkville Victoria 3052 Australia > > www.wehi.edu.au<http://www.wehi.edu.au> > > Twitter | Facebook | Instagram | Youtube | LinkedIn > > > > WEHI acknowledges the Wurundjeri people of the Kulin Nation as the > traditional owners of the land where our campuses are located and the > continuing connection to country and community. > > Private and confidential > The content of this e-mail and any attachments may be private and > confidential, intended only for use of the individual or entity named. 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