Hi Eleanor Thanks for catching that..
I was under the impression that when I am fetching the monomer, MDO, it was defined as a peptide, not a non polymer … at least that’s what is listed here: https://www.rcsb.org/ligand/MDO I guess I have to go about as Paul suggested as changing it to “peptide” Is an alternative using the PDB MDO cif file as the restraint as it is properly defined and replacing the original definition? -- Kelvin Lau Protein production and structure core facility - PTPSP 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 34494 On 21 Sep 2023, at 22:56, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: And in fact it doesnt.. data_comp_list loop_ _chem_comp.id<http://chem_comp.id> _chem_comp.three_letter_code _chem_comp.name<http://chem_comp.name> _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level MDO MDO "{2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid" NON-POLYMER 24 14 . # On Thu, 21 Sept 2023 at 21:53, Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote: Check the dictionary has labelled it as peptide like ALA data_comp_list loop_ _chem_comp.id<http://chem_comp.id> _chem_comp.three_letter_code _chem_comp.name<http://chem_comp.name> _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level ALA ALA ALANINE peptide 13 6 . On Thu, 21 Sept 2023 at 18:58, Paul Emsley <pems...@mrc-lmb.cam.ac.uk<mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: On 21/09/2023 18:05, Kelvin Lau wrote: > Dear all > > I am having trouble with an unnatural ligand/amino acid. > > I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO > residue that replaces three residues in a series G-A-S-G-D to become G-MDO-D. > MDO is in the Coot library. > > I have been very used to replacing cysteines with CME with Modelling>Replace > residue. It works great, removes the OXT and all the other atoms, can use > real space refine directly. > > For this MDO residue I find that it correctly fetches from the dictionary, > however, I cannot refine it. Whenever I click on an atom and drag it just > blows up or the atom gets stuck. > > I have now opened up 6Q6H and 7TQR and tried to just refine the built in MDO > in those PDB, same thing happens. > > Does anyone have any ideas of what might be going on? Also in general for > modified residues/unnaturals. If you tell Coot that the group is a non-polymer it will believe you. Use the Restraints editor to change the group to "peptide" (not tested). Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT<http://www.jiscmail.ac.uk/COOT>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ________________________________ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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/
