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Note that the ligand coordinates are already selected under "Atomic model", and the dictionary for the ligand C8M is already selected in the "Geometry dictionary" field.Īs well as displaying the ligand, we also want to display our protein model.Click the Coot button (at the bottom of the screen) - this will start a new job that will open Coot to display the ligand created by AceDRG.Now open our newly created ligand in Coot: When the job has finished, a 2D representation of the ligand will be displayed using Coot's Lidia. It then performs conformer generation using RDKit, followed by final optimisation using REFMAC5. It will then consult the AceDRG tables in order to generate a full ligand description, including the restraints for the bonds, angles, etc. Click the "Run" button on the top-right of the interface to run the job.ĪceDRG will infer chemistry from the SMILES string - information about atomic connectivity and bond orders.Or alternatively copy and paste the SMILES string into the interface Specify the three letter code for the output monomer: C8M Specify to start from either the SMILES file c8m.smi.Open the "Make Ligand - Acedrg" task interface, which can be found in the Ligands module. Open the CCP4i2 GUI, and create a new project as appropriate.We will begin by using AceDRG to generate the required coordinates and description for the ligand: Generating Ligand Coordinates And Description From Within CCP4i2

Generating Ligand Coordinates And Description From Within CCP4i2.Please click these links to access the files and save them to your computer. c8m.smi - a SMILES file specifying the ligand chemistry.ligand_removed.mtz - the reflection data.ligand_removed.pdb - the model with PDB code 3DZ4, after removing the ligand.Rob Nicholls - Emsley - Long - Murshudov - this tutorial, from within CCP4i2 we will generate coordinates and description of a ligand from a SMILES string using AceDRG, use Coot to fit and the ligand into a macromolecular model, and refine the model using REFMAC5.Ī basic working knowledge of the CCP4i2 GUI is assumed.