This is probably a FLEV specific issue. Have you tried external software such as LigPlot+ or Schrodinger’s Maestro to see if they can better handle the modified residue ?
> Le 27 janv. 2022 à 01:03, Sergio A. Sampieri <sampieri...@gmail.com> a écrit : > > Greetings all, > > Sorry for the naive question, but I'm having problems trying to FLEV a > modified residue in COOT. > > I have modeled a modified CYS into an structure following these steps: > > Generate a SMILES string for L-cysteine bonded the modification. > C1=CC=C(C=C1)C(=O)SCC(C(O)=O)N. > https://pubchem.ncbi.nlm.nih.gov/compound/262741 > <https://pubchem.ncbi.nlm.nih.gov/compound/262741> > Input the SMILES string to PHENIX eLBOW using the graphical user interface > with quantum optimization enabled to generate restraints (.cif) and > coordinates (.pdb). > Used the eLBOW graphical user interface to change the atom names for the > backbone atoms of the modified cysteine to the standard ones for amino acids > (N, CA, C, O, OXT, CB), (additional atom names remain as they are) > Save the new coordinates and restraints. > Modified the cif file, especially the definition as a L-peptide and not as > Ligand. > Move the modified cysteine saved in step 5 into the density using Coot. > Delete the extra OXT atom of the cysteine carboxylate and save the > coordinates of the modified Cys. > In coot "replace residue" CYS with the Modified CYS ("MCY"). > Refine the structure. > Open the refined model in COOT, and the cif dictionary generated. > > But when trying to FLEV the modified residue I get the next errors: > > WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for > atom name: " OXT" ele : O: > Failed to get atom index for atom name " OXT"" in residue of type MCY [spec: > 1 "A" 165 ""] > [17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted > std::exception > WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for > atom name: " OXT" ele : O: > Failed to get atom index for atom name " OXT"" in residue of type MCY [spec: > 1 "A" 165 ""] > [17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted > std::exception > WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for > atom name: " OXT" ele : O: > ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index > for atom name " OXT"" in residue of type MCY [spec: 1 "A" 165 ""] > > Also tried to modify the atom names in the CIF file but still get the same > error (with different atom numbers instead of OXT, O09 and so): > > WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for > atom name: " C10" ele : C: > ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index > for atom name " C10"" in residue of type MCY [spec: 1 "A" 165 ""] > > Any help or ideas would be greatly appreciated, thanks in advance, stay safe! > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> Xavier Brazzolotto, PhD Département de Toxicologie et Risques Chimiques Institut de Recherche Biomédicale des Armées BP 73 91223 Brétigny sur Orge France Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
