grade, the Global Phasing restraint dictionary generator


Introduction to grade

grade tries to use as much good chemical knowledge as possible to produce dictionaries. It was released to beta users on 8 October 2010 and to Academic 20 July 2011.

  • The best source of information about the stereochemistry of proteins, nucleic acids and ligands is the Cambridge Structural Database (the CSD). The CSD is a repository that contains over 500 000 small molecule structures.
  • The Engh and Huber restraints that BUSTER (and practically everyone else) use to restrain bonds and bond angles in protein were based on surveying CSD structures.
  • grade normally runs the CCDC Mogul program (in batch mode) to obtain ideal bond lengths/sigma, bond angles/sigmas and planar torsions from similar structures in the CSD. So these restraints are really compatible with Engh and Huber restraints used on the protein.
  • In practice mogul does not provide information for all restraint parameters needed because some chemical groups are rare or absent from the CSD. In addition mogul does not provide analysis of features involving hydrogen atoms or torsions within rings. To obtain the missing information, geometry optimization using a quantum chemical method in combination with mogul-based restraints is used. grade uses the RM1 semiempirical method as implemented in the fdynamo library written by Martin Field and co-workers.
  • If you do not have access to mogul, you can run grade -nomogul. In this case all the restraint information will be obtained from the results of an optimisation of the structure using the RM1 quantum method.
    • We find that, without the extra restraints provided by mogul, RM1 can give systematic errors in bond angles of up to four or five degrees, and in bond lengths of up to 0.04 angstrom.
    • plane identification in -nomogul mode is not as good as with mogul. It is a good idea to check the output dictionary with the EditREFMAC tool and check the planes are sensible.
  • grade sets torsion restraints where it is confident that they are sensible, for instance 3-fold torsions in aliphatic chains. BUSTER uses these in refinement and they can be turned on in coot
  • To get a grade-produced dictionary for an existing PDB ligand, use the grade_PDB_ligand tool and give it the three-letter code.
    • This connects to the RCSB LigandExpo server, downloads information about the ligand, and runs grade.
    • grade_PDB_ligand also has a -nomogul option.
  • grade will produce dictionaries from a number of input formats, such as SMILES and mol2 (see GradePreferredInputFormat).
    • grade uses the CCP4 libcheck program to do SMILES to 3D conversion but then works out the chemistry of the result by itself.
  • grade has been well received by our users in pharmaceutical research groups, who are sensitive about ligand restraints!

Page by Oliver Smart and Tom Womack original version 23 January 2011. Address problems, corrections and clarifications to buster-develop@globalphasing.com