Lorrie - life is getting more complicated every day! On Thu, 21 Sep 2023 at 23:39, Lucrezia Catapano < 0000ade43f7741e4-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi Kelvin, > > the 'group' in the monomer library do not necessarily correspond to the > 'type' in CCD. The reason was that stricter rules for peptides and other > groups were applied to the library. > > For MDO, there are 2 links: MDO-pept and pept-MDO to deal with this in a > polypeptide. > > Of course, you could force it to be peptide but maybe this should be > dealt with using specific links (that are in the monomer library). > > Lucrezia > > > > > > *From: *Mailing list for users of COOT Crystallographic Software < > COOT@JISCMAIL.AC.UK> on behalf of Kelvin Lau < > 00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> > *Date: *Thursday, 21 September 2023 at 22:25 > *To: *COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK> > *Subject: *Re: MDO Unnatural modified Amino acid > > You don't often get email from > 00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk. Learn why this is important > <https://aka.ms/LearnAboutSenderIdentification> > > 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 <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 > _chem_comp.three_letter_code > _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> > wrote: > > Check the dictionary has labelled it as peptide > > like ALA > > data_comp_list > loop_ > _chem_comp.id > _chem_comp.three_letter_code > _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> > 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, a mailing > list hosted by 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 > > ------------------------------ > > 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/
