Copyright (C) 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. 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 Ltd (bdg) running "grade -checkdeps" ERROR for tool 'mogul' cannot find the program on your PATH (the alternative is to define as environment variable '$BDG_TOOL_MOGUL'). N.B. you can run grade without mogul by using option -nomogul or by setting $BDG_TOOL_MOGUL to "none" ERROR for ccp4 tool 'libcheck' cannot find executable '/Applications/ccp4-6.4.0/bin/libcheck'. ccp4 utility libcheck needed and should be found from $CBIN ERROR there are 2 problems with external tools. See lines beginning "ERROR" above. Run "grade -checkdeps" to help sort out external packages etc. See /Users/software/GPhL/BUSTER_20130304/docs/installation/index.html for help ERROR termination because of dependencies failure ############################################################################ ## [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 'obabel' to '/usr/local/bin/obabel' from your $PATH rather than from $BDG_TOOL_OBABEL running "grade_PDB_ligand -checkdeps" ERROR for tool 'mogul' cannot find the program on your PATH (the alternative is to define as environment variable '$BDG_TOOL_MOGUL'). N.B. you can run grade without mogul by using option -nomogul or by setting $BDG_TOOL_MOGUL to "none" ############################################################################ ## [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 'obabel' to '/usr/local/bin/obabel' from your $PATH rather than from $BDG_TOOL_OBABEL check obabel version by '/usr/local/bin/obabel -V' yields 'Open Babel 2.3.1 -- Oct 13 2011 -- 15:14:48' Good obabel version '2.3.1' is newer than 2.1 ERROR for ccp4 tool 'libcheck' cannot find executable '/Applications/ccp4-6.4.0/bin/libcheck'. ccp4 utility libcheck needed and should be found 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" ERROR there are 2 problems with external tools. See lines beginning "ERROR" above. Use grade_PDB_ligand -checkdeps to help sort out dependencies. See /Users/software/GPhL/BUSTER_20130304/docs/installation/index.html for help ERROR termination because of dependencies failure running "hydrogenate -checkdeps" ERROR for tool 'reduce' cannot find the program on your $PATH Set $BDG_TOOL_MOLPROBITY_ROOT to the location of the MolProbity root installation ERROR cannot find reduce tool on your PATH it is needed for hydrogenate ############################################################################ ## [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 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 $BDG_TOOL_PDFLATEX to be "none" ERROR for tool 'convert' cannot find the program on your PATH (the alternative is to define as environment variable '$BDG_TOOL_CONVERT'). The convert tool (part of ImageMagick) is always needed. Please install it. ERROR for tool 'identify' cannot find the program on your PATH (the alternative is to define as environment variable '$BDG_TOOL_IDENTIFY'). The identify tool (part of ImageMagick) is always needed. Please install it ERROR for tool 'gracebat' cannot find the program on your PATH (the alternative is to define as environment variable '$BDG_TOOL_GRACEBAT'). The gracebat tool, part of xmgrace is needed (no exceptions) ERROR for tool 'ps2pdf' cannot find the program on your PATH (the alternative is to define as environment variable '$BDG_TOOL_PS2PDF'). The ps2pdf tool (part of Ghostscript) is always needed. Please install it. ERROR for tool 'pdflatex' cannot find the program on your PATH (the alternative is to define as environment variable '$BDG_TOOL_PDFLATEX'). You can run buster-report without pdflatex by using option -nopdf or by setting $BDG_TOOL_PDFLATEX to "none" ERROR for tool 'mogul' cannot find the program on your PATH (the alternative is to define as environment variable '$BDG_TOOL_MOGUL'). N.B. you can run buster-report without mogul by using option -nomogul or by setting $BDG_TOOL_MOGUL to "none" ERROR for tool 'pymol' cannot find the program on your PATH (the alternative is to define as environment variable '$BDG_TOOL_PYMOL'). N.B. you can run buster-report without pymol by using option -nopic or by setting $BDG_TOOL_PYMOL to "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 "5.12.4" successfully loaded perl module IPC::Cmd version 0.54 successfully loaded perl module CGI version 3.51 successfully loaded perl module File::Basename version 2.78 successfully loaded perl module File::Temp version 0.22 successfully loaded perl module File::Copy version 2.18 successfully loaded perl module Params::Check version 0.26 Setting tool 'obabel' to '/usr/local/bin/obabel' from your $PATH rather than from $BDG_TOOL_OBABEL 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_65",,,Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609),,,Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)' success as java -version does not contain 'gcj' MolProbity tool location environment vble $BDG_TOOL_MOLPROBITY_ROOT has not been set so setup from $PATH instead: ERROR for tool 'reduce-nobuild' cannot find the program on your $PATH Set $BDG_TOOL_MOLPROBITY_ROOT to the location of the MolProbity root installation You can run buster_report without reduce-nobuild by using option -nomp or by setting $BDG_TOOL_MOLPROBITY_ROOT to "none" ERROR for tool 'multichart' cannot find the program on your $PATH Set $BDG_TOOL_MOLPROBITY_ROOT to the location of the MolProbity root installation You can run buster_report without multichart by using option -nomp or by setting $BDG_TOOL_MOLPROBITY_ROOT to "none" ERROR for ccp4 tool 'fft' cannot find executable '/Applications/ccp4-6.4.0/bin/fft'. ccp4 utility fft needed and should be found from $CBIN ERROR for ccp4 tool 'mapmask' cannot find executable '/Applications/ccp4-6.4.0/bin/mapmask'. ccp4 utility mapmask needed and should be found from $CBIN Setting tool 'corr' to '/Users/software/GPhL/BUSTER_20130304/autoBUSTER/bin/darwin/corr' from your $PATH ERROR there are 11 problems with external tools. See lines beginning "ERROR" above. See /Users/software/GPhL/BUSTER_20130304/docs/installation/index.html for help ERROR termination because of dependencies failure 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 ==== ERROR: You do not have CCP4 correctly set up. You will not be able to run Pipedream. Please check your GPhL and CCP4 software installations! 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 00:37:57>) is correctly set up in /Users/software/GPhL/BUSTER_20130304. SUCCESS: Rhofit (version 1.2.3 <2012-11-26> ) is correctly set up in /Users/software/GPhL/BUSTER_20130304. WARNING: buster-report dependency checks failed. Pipedream will not run buster-report. Please run "buster-report -checkdeps" for more information. FAIL: Pipedream dependency checks have failed. There is 1 error that needs to be addressed! checkdeps FINAL SUMMARY refine (licence): SUCCESS grade: FAIL grade_PDB_ligand: FAIL hydrogenate: FAIL buster-report: FAIL pipedream: FAIL