PS: If you have two different home-brewn ligands, you have to rename one of them (pdb and cif), otherwise the same dictionary will be applied to two different ligands. Also make sure your cif file is a dictionary and not just a coordinate file. HS
Von: Schreuder, Herman /DE Gesendet: Montag, 5. März 2018 14:31 An: 'Colin Levy'; CCP4BB@JISCMAIL.AC.UK Betreff: AW: [ccp4bb] Small molecule not refined in coot. Hi Colin and Michel, In my experience, both refmac and coot will use the most recently read-in cif dictionary and there is no need to try to find an unique identifier for each new ligand one uses. The new dictionary overrides the old one. Finding a unique identifier for each new ligand would be a terrible and unnecessary hassle. What usually goes wrong is that the name of the residue in the pdb file does not match the name of the residue in the cif file. And the same holds for the atom names. I would check with an editor that the resdue and atom names of the pdb file do match the residue and atom names in the cif dictionary. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Colin Levy Gesendet: Montag, 5. März 2018 13:38 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [EXTERNAL] Re: [ccp4bb] Small molecule not refined in coot. Hi Michel, If your ligand is designated as DRG in your pdb then refinement programs will anticipate that it is: Chemical Description Name 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE Formula C12 H11 N3 Formal charge 0 Molecular weight 197.236 g/mol Component type NON-POLYMER If this is not the case then you need to choose a unique identifier, this should then allow your cif library to be utilised appropriately during refinement. Colin [cid:image001.png@01D3B48F.5E6EF790] Dr. Colin W. Levy MIB G016 Tel. 0161 275 5090 Mob.07786 197 554 c.l...@manchester.ac.uk<mailto:c.l...@manchester.ac.uk> Manchester Institute of Biotechnology | University of Manchester | 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN [cid:image002.png@01D3B48F.5E6EF790]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_MIB2006_-3Fref-3Daymt-5Fhomepage-5Fpanel&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=bKUGrH6wK5dQ2KLRw6oxFvnOjjWsZxfqbmZabgHnlnE&e=>[cid:image003.png@01D3B48F.5E6EF790]<https://urldefense.proofpoint.com/v2/url?u=https-3A__plus.google.com_u_0_b_111834792186886067949_111834792186886067949_posts-3F-5Fga-3D1.142941878.209859079.1446729440&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=MxPD1QWp-GEhbvwGRdaEozWff1HvapFjYoa0O8j8ARY&e=>[cid:image004.png@01D3B48F.5E6EF790]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_company_manchester-2Dinstitute-2Dof-2Dbiotechnology-3Ftrk-3Dbiz-2Dcompanies-2Dcym&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=NX4ub_6zOoHnKdhhIKKDNhy_ubtCXCpBDqtdRB6ChmM&e=>[cid:image005.png@01D3B48F.5E6EF790]<https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_-3Flang-3Den-2Dgb-26lang-3Den-2Dgb&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=gNH6h2r1l3Fb1ho0UL9pWdjiU7yWfDS8tojGhnLoQE4&e=>[cid:image006.png@01D3B48F.5E6EF790]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_channel_UCCBV8zDxk4L9yOEcujvSFNw&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=z2OpzMpJB9EYcL5yPECYcsocmhXktsEK-N_415fT35g&e=> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_channel_UCCBV8zDxk4L9yOEcujvSFNw&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=2Ib8W-dQ0MHoUt4AHNaero85sr0-ZRZXc93QBAWf108&s=z2OpzMpJB9EYcL5yPECYcsocmhXktsEK-N_415fT35g&e=> On 5 Mar 2018, at 12:30, M T <michel...@gmail.com<mailto:michel...@gmail.com>> wrote: Dear all, I am actually dealing with a structure containing an unnatural ligand. I generated the pdb file by drawing it on PRODRG server, I did a manual pre-fit in the map using coot and I manually merged the pdf file of my protein with the one of the ligand. After that I did few cycles of refinement using Refmac5, with my mtz, my merged pdb file and the cif library of the ligand as input files. First I saw that even if Refmac "completed succesfully" it didn't modify coordinates of the ligand, second I saw a warning about the "DRG" molecule in the log of Refmac (WARNING: duplicated name of monomer DRG Last entry will be used.), third in Coot I cannot use "Real Space Refine Zone" with the ligand and when I try to import the CIF dictionary produced by PRODRG (through the server or even the one generated through CCP4 ProDrg), it causes Coot crash (** (coot-bin:4467): WARNING **: Widget not found: cif_dictionary_file_selector_create_molecule_checkbutton /programs/i386-mac/ccp4/7.0/ccp4-7.0/bin/coot: line 288: 4467 Segmentation fault: 11 $coot_bin "$@"). Clearly I am not a skilled user of all these programs, so I certainly did a/some mistake/s, but if someone can give me tips to be able to refine my ligand... Should I rename my DRG molecule, should I verify particular things, should I use other ways to generate the pdb and the library of my ligand? Thank you. P.S.: I am running CCP4 and coot using SBGRID on a Mac. Michel
