N.B. This page is for old versions of buster-report. Please ignore and instead follow the detailed installation instructions available from your BUSTER download page or in file:
$BDG_home/docs/installation/index.html
Note added June 2014
buster-report is a tool to provide clear, short reports of how a BUSTER run has proceeded, and an analysis of the final result. It uses a wide variety of standard scientific-software tools to perform the analysis. This page is to help with setting up these packages.
| software tool name | version number | command run by buster-report (needs to be on users PATH variable) | required or optional? |
| xmgrace | tested with 1:5.1.22-9 ubuntu | gracebat | required (needed to plot graphs). |
| ghostscript | ps2pdf | required (needed to produce graphs) | |
| ImageMagick | convert | required (needed for graphics file conversions) | |
| LaTeX | pdflatex | optional, only needed for PDF output with the -pdf option | |
| PyMol | works well 1.4.1 compiled from source following http://www.pymolwiki.org/index.php/Linux_Install Works but some problems with 1.2r2 (bundled with ubuntu) | pymol | optional. Use -nopic option to turn off molecular pictures. |
| mogul | tested with 2011, 2012 and 2013 CSD System releases. See SoftwareMogulRelease2013Issue | mogul this must the CSD supplied command and not an alias or a wrapper script. | optional. Turn off by -nolig option (turns off all ligand analysis). In case of mogul problems make sure that the interactive mogul program runs. |
| MolProbity | tested with 3.19.110929 | remark40, reduce hless.jar (for Ramachandran plots) | optional. Turn off MolProbity analysis with -nomp option. |
| Openbabel | Tested from version 2.2.1 on | obabel | optional but recommended |
% sudo apt-get install grace pymol imagemagick
% sudo apt-get install php5-cli gawk
% sudo apt-get install texlive-latex-extra
There is an issue with the build of grace supplied with Ubuntu 12.04 which will result in unreadable svg plots - the Rfactor plot and RSCC plots on the main buster-report page will be mangled.
To fix this issue:
% sudo apt-get install libpng-dev
% tar xf grace-latest.tar.gz % cd grace-5.1.23
/home/software/grace)
% ./configure prefix=/home/software/grace
% make ; make install
Stop Press: 1st November 2012. We submitted a bug report to Ubuntu / Debian. The problem has been recognized and fixed and a corrected version released for upcoming Ubuntu release 13.04 (not due until April 2013). At present corrected versions have not been released for 12.04 lts or 12.10. We have requested backports to 12.04 and 12.10.
% sudo apt-get install ia32-libs
% sudo apt-get install imagemagick openbabel pymol
% sudo apt-get install curl
% sudo apt-get install php5-cli gawk % sudo apt-get install openjdk-6-jre openjdk-7-jre icedtea6-plugin
% sudo apt-get install texlive-latex-extra
Installation of xmgrace, ghostscript, LaTeX and ImageMagick:
% zypper install ghostscript-x11 xmgrace ImageMagick texlive-latex
To install Pymol:
% zypper addrepo http://download.opensuse.org/repositories/devel:languages:python/openSUSE_11.3/devel:languages:python.repo % zypper refresh % zypper install pymol
The openbabel package included in the OpenSuSE 11.4 repository is incomplete and flawed. It does not include the obabel binary and the included babel binary is compromised.
You will need to download the openbabel source code from the openbabel web site and compile locally.
% su -c 'rpm -Uvh http://download.fedoraproject.org/pub/epel/5/i386/epel-release-5-4.noarch.rpm' % yum install grace
Page by Andrew Sharff and Oliver Smart original version 1 Dec 2011, revised May 2013. Address problems, corrections and clarifications to buster-develop@globalphasing.com
