Hi, as previously suggested you can use AceDRG to generate a cif file for your ligand by input different type of files (SMILES, mmCIF, SDF/MOL, and SYBYL MOL2 files).
You can use the AceDRG command line: https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/acedrg/acedrg.html or via ccp4i2, 'Ligands' menu, 'make ligand-AceDRG'. Regards Lucrezia > Dear CCP4 Users, > > I am working with data containing a possible complex of protein with > FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this > ligand is not available in PDB. The closest molecule is COSAN (cobalt > bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two > PDB entries. I can load this molecule into Coot, but attempts at ligand > search or refinement of the manually matched molecule result in freezing > of the Coot window. FESAN is not present in CCDC as a single molecule, > but only in some complexes. Could you give me some advice on how to > prepare a new ligand like this one, for incorporation into the protein > and further refinement? > > Best regards, > > Rafal Dolot > > -- > |----------------------------------------------| > |Rafal Dolot, Ph.D. | > | | > |Polish Academy of Sciences | > |Centre of Molecular and Macromolecular Studies| > |Division of Bioorganic Chemistry | > |Macromolecular Crystallography Laboratory | > |Sienkiewicza 112 | > |90-363 Lodz, Poland | > |Phone: +48(42)6803325 | > |Cell: +48 502897781 | > |----------------------------------------------| > > ######################################################################## > > 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/ > Lucrezia Catapano PhD student Murshudov Group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom ######################################################################## 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/
