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: 1. 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 2. Input the SMILES string to PHENIX eLBOW using the graphical user interface with quantum optimization enabled to generate restraints (.cif) and coordinates (.pdb). 3. 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) 4. Save the new coordinates and restraints. 5. Modified the cif file, especially the definition as a L-peptide and not as Ligand. 6. Move the modified cysteine saved in step 5 into the density using Coot. 7. Delete the extra OXT atom of the cysteine carboxylate and save the coordinates of the modified Cys. 8. In coot "replace residue" CYS with the Modified CYS ("MCY"). 9. Refine the structure. 10. 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 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/
