Copyright (C) 2013-2014 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. Authors: Smart OS, Sharff A, Flensburg C, Keller P, Paciorek W, Vonrhein C and Bricogne G ======================== checkdeps utility script ======================== This is an interactive script that will check programs in the BUSTER suite in turn. It makes sure that all the required 3rd party tools are installed, available and function properly. Problems are indicated on lines starting "ERROR". If no problems are found then this is shown by "SUCCESS" By default this script will prompt before running each test. To turn off prompting use option "-n". check refine licence OK by "refine -h | grep licenced" # This software is licenced to : Global Phasing (fuji01vm) running "grade -checkdeps" ############################################################################ ## [grade] produce ligand dictionary using mogul and QM methods ############################################################################ 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, Holstein, J, 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/ -checkdeps option: verbose dependencies check for required external tools with tests all tools work properly. Setting tool 'mogul' to '/home/software/cambridge/bin/mogul' from environment variable $BDG_TOOL_MOGUL test mogul by asking for bond angle of CO2 .. Run mogul with generalisation_min_relevance=0.9 for bond and angle SUCCESS found 99 angles with mean 173.62 degs, CSD='as535be' mogul version='1.6 (RC5)' Setting tool 'obabel' to '/usr/bin/obabel' from your $PATH rather than from $BDG_TOOL_OBABEL Setting ccp4 tool 'libcheck' to '/software/ccp4/destination/ccp4-6.4.0/bin/libcheck' from $CBIN SUCCESS grade -checkdeps indicates that everything needed to run grade works fine running "grade_PDB_ligand -checkdeps" ############################################################################ ## [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/ -checkdeps option: verbose dependencies check for required external tools with tests all tools work properly. Setting tool 'mogul' to '/home/software/cambridge/bin/mogul' from environment variable $BDG_TOOL_MOGUL test mogul by asking for bond angle of CO2 .. Run mogul with generalisation_min_relevance=0.9 for bond and angle SUCCESS found 99 angles with mean 173.62 degs, CSD='as535be' mogul version='1.6 (RC5)' Setting tool 'obabel' to '/usr/bin/obabel' from your $PATH rather than from $BDG_TOOL_OBABEL check obabel version by '/usr/bin/obabel -V' yields 'Open Babel 2.3.0 -- Dec 17 2011 -- 16:15:10' Good obabel version '2.3.0' is newer than 2.1 Setting ccp4 tool 'libcheck' to '/software/ccp4/destination/ccp4-6.4.0/bin/libcheck' from $CBIN Setting tool 'curl' to '/usr/bin/curl' from your $PATH rather than from $BDG_TOOL_CURL N.B. will use curl rather than wget. No curl additional command line options specified as $BDG_TOOL_CURL_OPTIONS not defined. Test download of http://ligand-expo.rcsb.org/reports/M/MOH/MOH.cif .. Gets 3981 characters, as expected. Success as it contains "_chem_comp.id" Test download of ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/mmcif/MOH.cif .. Gets 3981 characters, as expected. Success as it contains "_chem_comp.id" SUCCESS grade_PDB_ligand -checkdeps indicates that everything needed to run grade_PDB_ligand works fine running "hydrogenate -checkdeps" ############################################################################ ## [hydrogenate] use MolProbity reduce with cif dictionaries ############################################################################ Copyright (C) 2011-2013 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: 1.1.0 Authors: Smart OS, Womack, TO, Sharff A, Flensburg C, Keller P, Paciorek W, Vonrhein C and Bricogne G ------------------------------------------------------------------------------ Acknowledgements: hydrogenate uses the 'reduce' tool; if you publish work which uses it, please cite Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747. For more information see http://kinemage.biochem.duke.edu reduce /home/software/molprobity/latest/bin/linux/reduce from $BDG_TOOL_MOLPROBITY_ROOT, -Version yields 'reduce.3.24.130724' SUCCESS hydrogenate -checkdeps indicates that everything needed to run hydrogenate works fine running "buster-report -checkdeps" ############################################################################## ## [buster-report] produce user-friendly report of a BUSTER run ############################################################################## Copyright (C) 2011-2014 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: 1.1.1a NOTE will produce pdf output with latex. Turn off by -nopdf or setting $BDG_TOOL_PDFLATEX to be "none" -checkdeps option: extended verbose dependencies check for required external tools with checks that they work properly. Checking the versions of essential perl modules: perl version number is "5.14.2" successfully loaded perl module IPC::Cmd version 0.70 successfully loaded perl module CGI version 3.52 successfully loaded perl module File::Basename version 2.82 successfully loaded perl module File::Temp version 0.22 successfully loaded perl module File::Copy version 2.21 successfully loaded perl module Params::Check version 0.28 Setting tool 'convert' to '/usr/bin/convert' from your $PATH rather than from $BDG_TOOL_CONVERT Setting tool 'identify' to '/usr/bin/identify' from your $PATH rather than from $BDG_TOOL_IDENTIFY Setting tool 'gracebat' to '/usr/bin/gracebat' from your $PATH rather than from $BDG_TOOL_GRACEBAT test gracebat function .PNG output ok, SVG output ok, success! Setting tool 'ps2pdf' to '/usr/bin/ps2pdf' from your $PATH rather than from $BDG_TOOL_PS2PDF Setting tool 'pdflatex' to '/usr/bin/pdflatex' from your $PATH rather than from $BDG_TOOL_PDFLATEX test pdflatex works on a simple test.tex input (tests all latex required packages are available) ..1.2.3.success Setting tool 'mogul' to '/home/software/cambridge/bin/mogul' from environment variable $BDG_TOOL_MOGUL test mogul by asking for bond angle of CO2 .. Run mogul with generalisation_min_relevance=0.9 for bond and angle SUCCESS found 99 angles with mean 173.62 degs, CSD='as535be' mogul version='1.6 (RC5)' Setting tool 'obabel' to '/usr/bin/obabel' from your $PATH rather than from $BDG_TOOL_OBABEL Setting tool 'pymol' to '/usr/bin/pymol' from your $PATH rather than from $BDG_TOOL_PYMOL Setting tool 'java' to '/usr/bin/java' from your $PATH rather than from $BDG_TOOL_BUSTERREPORT_JAVA check 'java -version' yields 'java version "1.6.0_27",,,OpenJDK Runtime Environment (IcedTea6 1.12.5) (6b27-1.12.5-0ubuntu0.12.04.1),,,OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)' success as java -version does not contain 'gcj' MolProbity tool location from $BDG_TOOL_MOLPROBITY_ROOT set to '/home/software/molprobity/latest' will setup tools from this: MolProbity reduce-nobuild is '/home/software/molprobity/latest/cmdline/reduce-nobuild' MolProbity multichart is '/home/software/molprobity/latest/cmdline/multichart' MolProbity hless.jar library is '/home/software/molprobity/latest/lib/hless.jar' test run that MolProbity 'reduce-nobuild' can be executed with no input. Success got expected output 'No input directory specified.' test run that MolProbity 'multichart' can be executed with no input. Success got expected output 'No input file specified.' test run MolProbity 'multichart' works fully on test3residues.pdb input .(v4-4.01a+).success! test run MolProbity Ramachandran plot png production..success! Setting ccp4 tool 'fft' to '/software/ccp4/destination/ccp4-6.4.0/bin/fft' from $CBIN Setting ccp4 tool 'mapmask' to '/software/ccp4/destination/ccp4-6.4.0/bin/mapmask' from $CBIN Setting tool 'corr' to '/home/software/GPhL/BUSTER_snapshot_20140304/autoBUSTER/bin/linux64/corr' from your $PATH SUCCESS buster-report -checkdeps indicates that everything needed to run buster-report works fine running "pipedream -checkdeps" ############################################################################## ## [pipedream] Automatic data processing and structure refinement ############################################################################## Copyright (C) 2011-2014 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: 0.1.5 <2014-03-04> ------------------------------------------------------------------------------ Authors: Sharff A, Keller P, Vonrhein C, Smart O, Womack T, Flensburg C, Paciorek W, Bricogne G (2011). Pipedream version 0.1.5. Global Phasing Ltd., Cambridge, United Kingdom. Contact: buster-develop@globalphasing.com ============================================================================== ==== Check Pipedream installation and dependencies ==== SUCCESS: Pipedream has found CCP4 version 6.4.0, installed in /software/ccp4/destination/ccp4-6.4.0 WARNING: autoPROC is not installed. You will not be able to run Pipedream with unprocessed data! SUCCESS: BUSTER (version 1.11.5 <2014-03-04 00:41:23>) is correctly set up in /home/software/GPhL/BUSTER_snapshot_20140304. SUCCESS: Rhofit (version 1.2.3 <2012-11-26> ) is correctly set up in /home/software/GPhL/BUSTER_snapshot_20140304. SUCCESS: buster-report (version 1.1.1a ) is correctly set up in /home/software/GPhL/BUSTER_snapshot_20140304. SUCCESS: Pipedream is correctly set up. Enjoy! checkdeps FINAL SUMMARY refine (licence): SUCCESS grade: SUCCESS grade_PDB_ligand: SUCCESS hydrogenate: SUCCESS buster-report: SUCCESS pipedream: SUCCESS