############################################################################ ## [grade_PDB_ligand] produce grade dictionary for existing PDB ligand ############################################################################ Copyright (C) 2010-2014 by Global Phasing Limited All rights reserved. This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL. Version: 1.2.7 Authors: Smart OS, Womack, TO, Sharff A, Flensburg C, Keller P, Paciorek W, Vonrhein C and Bricogne G To cite: see http://www.globalphasing.com/buster/wiki/index.cgi?GradeCite ------------------------------------------------------------------------------ Acknowledgements: mogul: http://www.ccdc.cam.ac.uk/products/csd_system/mogul/ libcheck: http://www.ccp4.ac.uk/html/libcheck.html QM method uses fdynamo library http://www.pdynamo.org/ to perform calculations using the RM1 method http://www.rm1.sparkle.pro.br/ Setting up external tools needed....(obabel version 2.3.1)..(curl=/usr/bin/curl). Success all external tools are properly setup (for a more thorough check run "grade_PDB_ligand -checkdeps"). Looking for 468 at EBI MSDchem Ligand name: 468 is _3S_-N-_3-CHLORO-2-METHYLPHENYL_-1-CYCLOHEXYL-5-OXOPYRROLIDINE-3-CARBOXAMIDE Converting downloaded ideal pdb to mol2 using obabel version 2.3.1 : 1 molecule converted Now invoking grade to get dictionary: Setting up external tools needed.(test mogul).. Success all external tools are properly setup (for a more thorough check run "grade -checkdeps"). Loading atom-type information from /home/software/GPhL/BUSTER_beta_20140220/autoBUSTER/grade-data/sybyl_to_refmac.dat Loading atom-type information from /home/software/GPhL/BUSTER_beta_20140220/autoBUSTER/grade-data/sybyl_to_refmac.dat Input is MOL2; assuming that the coordinates in the mol2 are good Run mogul with generalisation_min_relevance=0.9 for bond and angle mogul ran (cpu secs used: 6.0 real, 4.1 user, 0.1 sys) Loaded hybridisations for 55 atom types from /home/software/GPhL/BUSTER_beta_20140220/autoBUSTER/grade-data/ccp4_atomtype_hybridisation.dat Adding new plane C9 C12 N13 C15 suggested by mogul Assuming molecule is uncharged Fixing up pseudochirals for MOL2 found 9 pseudochiral centre(s); marking them as 'both' Method details: "MOGUL 1.6(RC5), CSD as535be, with quantum mechanics RM1" Now running recognise-compound utilty to check whether the ligand is a known PDB chemical component. recognise-compound 468.grade_PDB_ligand.pdb results in "Input is known PDB chemical component "(3s)-n-(3-chloro-2-methylphenyl)-1-cyclohexyl-5-oxopyrrolidine-3-carboxamide" with three-letter code 468" Generated CIF 468.grade_PDB_ligand.cif and PDB 468.grade_PDB_ligand.pdb Use the command EditREFMAC 468.grade_PDB_ligand.cif 468.grade_PDB_ligand.pdb 468 to view and edit this dictionary (cpu secs used: 48.1 real, 44.4 user, 4.8 sys)