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:3A59087A-E871-4A15-8C7F-384F6788170E@man.ac.uk] 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:image001.png@01D11BB1.F717D2B0]<https://www.facebook.com/MIB2006/?ref=aymt_homepage_panel>[cid:image002.png@01D11BB1.F717D2B0]<https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/posts?_ga=1.142941878.209859079.1446729440>[cid:image003.png@01D11BB1.F717D2B0]<https://www.linkedin.com/company/manchester-institute-of-biotechnology?trk=biz-companies-cym>[cid:image004.png@01D11BB1.F717D2B0]<https://twitter.com/?lang=en-gb&lang=en-gb><https://twitter.com/?lang=en-gb&lang=en-gb>[cid:image005.png@01D11BB1.F717D2B0]<https://www.youtube.com/channel/UCCBV8zDxk4L9yOEcujvSFNw><https://www.youtube.com/channel/UCCBV8zDxk4L9yOEcujvSFNw> <https://www.youtube.com/channel/UCCBV8zDxk4L9yOEcujvSFNw><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/posts?_ga=1.142941878.209859079.1446729440><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/posts?_ga=1.142941878.209859079.1446729440><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/posts?_ga=1.142941878.209859079.1446729440> 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