Tip These instructions are for CentOS 7.x 64bit,
Generic snapshot BUSTER release date 20240123.

Please note this version of BUSTER is for academic users and its download, installation and use is conditional on acceptance of the licence conditions. Please carefully review these licence conditions before download, installation or use.

1. Introduction

  • These instructions have been prepared on a workstation running an updated CentOS 7 x86_64 (64 bit) version. They should work for all 64 bit CentOS and RHEL 7.x versions.

  • Please first check that the machine where you are doing the installation is actually running under a 64 bit CentOS 7.x OS. To do this run the commands:

cat /etc/*-release; uname -m
CentOS Linux release 7.9.2009 (Core)

Tip This page uses green bold text for the commands you type, blue italic text for the output produced and red italics for comments. The command prompt is omitted to make copy/paste easier. Some long lines may be wrapped in your display but if you use copy and paste the commands should work fine.
  • If the commands do not result in reports of CentOS or Red Hat Enterprise Linux and a version 7.x (where x is a number) and x86_64 then you are looking at the wrong page! Please go back and select your OS.

  • Apart from step 2, installation is done from a user account software (without root privilege), using the bash shell and assuming that the browser downloads to the ~/Downloads directory.

  • You will probably have to adapt the procedure in places as you are likely to be installing in a different location and possibly with a different shell.

  • The following crystallographic packages are requirements for the use of BUSTER:

    • CCP4 Suite - required by all components of BUSTER

    • Cambridge Structural Database (CSDS) - not needed for structure refinement with BUSTER or ligand fitting with Rhofit, but required for dictionary generation with Grade/Grade2 and model analysis with buster-report

  • The following utility programs/packages are also required:

    • ImageMagick - required by buster-report

    • PyMOL - required by buster-report (we provide a binary for some operating systems)

    • TeX/LaTeX - required by buster-report (for PDF generation)

  • Instructions for installation of all of these programs/packages are given below. If you already have working installations of versions of the above packages that are compatible with BUSTER (see sections below for version information), then we would recommend that you use these installations and you may skip the corresponding section(s) below.

2. CentOS packages

CentOS package installation must be done as root.
  • Now download the list of packages that need to be installed gphl_package_list.txt (hint right click and select "Save Link As"). Then move the file into your current directory. To install the packages in the list:

xargs yum -y install < gphl_package_list.txt

  • Finally, we recommend that you ensure that the OS is up-to-date by applying OS-recommended updates (particular security patches). To do this issue the command:

yum update

  • Then reboot the machine if this is advised.

The rest of these instructions should be performed as an unprivileged user: NOT 'root'.
  • We will use a user account called software as an example, but you could also use any other normal user account.

3. CCP4 (and Coot)

Tip Skip this section if you already have a working CCP4 8.0 (and Coot) installation.
  • CCP4 should be installed in a non-root account (here software).

  • Coot is now automatically installed by the CCP4 package manager: you no longer need to install it separately.

  • Follow the link to http://www.ccp4.ac.uk and then select DOWNLOAD from the *SOFTWARE" pull-down menu.

    • The page starts Here you can download the latest version of the CCP4 Software Suite, version 8.0, code name Addingham.

    • Make sure you are looking at the GNU/Linux pane.

    • Then download the Package Manager (64 bit) using the orange Download Now! button.

    • Download the linux-8.0-setup.tar.gz file and unpack it in a directory ~/ccp4. These are my commands to do this:

mkdir ~/ccp4; cd ~/ccp4
tar xvf ~/Downloads/linux-8.0-setup.tar.gz

  • Now launch the CCP4 package manager GUI:


  • You should see the CCP4 Software Suite Setup: follow the instructions.

    • Select CCP4 Program Suite v8.0.

    • If you are a publically funded academic institution or you have a valid commercial SHELX licence: select SHELX.

    • If you are a publically funded academic institution or you have a valid commercial ARP/wARP licence: select ARP/wARP v8.0.

    • Agree to CCP4 terms and conditions (if not done before).

    • Confirm the ARP/wARP licence (if appropriate) and agree to its terms and conditions.

    • Set the location for the installation to ~/ccp4.

  • CCP4 package should be downloaded and installed: have a cup of coffee!

    • The installation process will automatically install all CCP4 updates available at the time of installation. Post-installation, we would strongly recommend that you keep your CCP4 installation updated by applying new updates as they are released by CCP4 (either through running ccp4i2, ccp4i or ccp4um).

  • If you want to test the installation see quick test of the CCP4 installation.

    • Test that the coot executable has been installed correctly by running it and verifying that the GUI works:


  • Optionally test that the ARP/wARP system has been installed correctly by running:

$warpbin/check_programs.sh $warpbin/auto_tracing.sh $warpbin
### You are running ARP/wARP 8.0 patch 1 ###

You must have a working installation of CCP4 before installing Global Phasing Software.
We strongly recommend that you keep your CCP4 installation updated by applying new updates as they are released by CCP4 either through running ccp4i2, ccp4i or ccp4um.

4. BUSTER installation

  • This section is omitted from the "Generic" pages included as files in the distribution because to see this page the install must have already been done.

  • For details please consult the specific page available at your download page, see https://www.globalphasing.com/

  • The last part of the output is important as it describes how users set up access to the software, (for example BUSTER-install-important-information-log.txt), see also section BUSTER user access .

  • At this stage of the installation you will have a working BUSTER refine.

  • If you want, this can be quickly tested by checking for licence information in the refine help message test-refine-licence-log.html.

Tip To get all Global Phasing Software working fully involves installing other packages and some further configuration as detailed below.

5. CSDS (mogul)

Tip Both grade2 and buster_report require the CCDC mogul program for full functionality. If you do not have access to CSDS software then you should set the environment variable $BDG_TOOL_MOGUL to none at the configure stage.
  • The current release version of the CSD at time of writing is CSD 2023 (2023.1), containing the Cambridge Structural Database (Version 5.44).

  • mogul is included as part of the CSD Core software (often called Cambridge Structural Database System, CSDS)) from CCDC. Please follow the instructions for CSD installation - see online instructions. It is assumed here that you install in the default location of ~/cambridge.

  • Following installation we would strongly recommend that you download and apply the latest CSD updates from the CCDC website.

Note There may be problems using mogul from CSDS 2021 Release v5.42 if CSDS is used from an NFS-mounted file system (particularly from an NFS v3 mounted file system), please see here or here for details.
  • Once you have installed the software, ensure that the CCDC licensing formalities are completed. The best way to do this is to start mogul in a X windows environment:


  • You should then be prompted by the GUI to enter your licence information.

6. BUSTER configure

  • This stage involves creating files setup_local.sh and setup_local.csh in the GPhL installation directory ~/GPhL/BUSTER_snapshot_20240123

  • The file setup_local.sh is sourced by the Global Phasing Software setup script setup.sh used by sh, bash and dash users (see BUSTER user access below).

  • The file setup_local.csh is sourced by the Global Phasing Software setup script setup.csh used by csh and tcsh users (see BUSTER user access below).

  • If all your users use the same shell then you only need to provide the appropriate script.

  • If you have a sophisticated environment with some software only licenced or available on certain machines then the setup_local.*sh files can use shell script tests to achieve this. Please ask for help if you need it.

  • In general setup_local.sh and/or setup_local.csh once created will work for future releases and can be simply copied from the previous installation.

  • Please use the files we produced while writing these instructions for CentOS 7.x 64bit:

    • Download file setup_local.sh and save it as
      ~/GPhL/BUSTER_snapshot_20240123/setup_local.sh .

    • Download file setup_local.csh and save it as
      ~/GPhL/BUSTER_snapshot_20240123/setup_local.csh .

    • These files have been produced from the template files provided in ~/GPhL/BUSTER_snapshot_20240123/samples/setup_local.sh and ~/GPhL/BUSTER_snapshot_20240123/samples/setup_local.csh where all the options that can be set are described in comments.

  • For this CentOS 7.x installation the only lines that must be set are those for the environment variables BDG_TOOL_MOGUL . For instance, in the file setup_local.sh the only non-comment lines are:

export BDG_TOOL_MOGUL=~software/cambridge/bin/mogul
  • If you have installed all the packages above in exactly the same place as suggested above then no editing of $BDG_home/setup_local.sh and $BDG_home/setup_local.csh should be required.

  • Now test the installation as described in the Testing section.

  • If checkdeps reports ERRORs then you will have to modify $BDG_home/setup_local.sh and/or $BDG_home/setup_local.csh. To do so use your favourite editor (emacs, vi, jot, gedit, …), then test again.

  • If you have a firewall with a proxy that prevents curl from directly downloading information then you will need to set environment variable $BDG_TOOL_CURL_OPTIONS. Use a web browser (firefox) to look at the External tools section of the grade manual: $BDG_home/docs/grade/manual/index.html for more information.

7. BUSTER test install

  • We supply checkdeps: a tool that checks that the dependencies of all our programs are met. In addition checks are made that each 3rd party program works properly.

  • To run checkdeps:

    1. open a new terminal or shell,

    2. then invoke the GPhL setup script (see useraccess), and

    3. enter the command checkdeps at the shell prompt.

  • For instance, if you are a bash user then:

. ~/GPhL/BUSTER_snapshot_20240123/setup.sh

  • You will be prompted before each individual program is checked, unless you run

. ~/GPhL/BUSTER_snapshot_20240123/setup.sh
checkdeps -n

  • The checks should take about 10 seconds cpu.

  • The program is deliberately verbose to provide full details about your setup to be included in bug reports. But note that checkdeps finishes with a simple summary of results:

     refine (licence):     SUCCESS
     grade:                SUCCESS
     grade_PDB_ligand:     SUCCESS
     hydrogenate:          SUCCESS
     buster-report:        SUCCESS
     grade2:               SUCCESS
     pipedream:            SUCCESS
  • If a FAIL was reported then look through the output for the lines that start with ERROR. For instance if the configuration step has not been carried out then checkdeps will produce output similar to: checkdeps-log-fail.txt .

Note If you have installed and set up autoPROC separately checkdeps will also check that the autoPROC command process functions correctly (since pipedream may use it).
  • If the installation and configuration has been completed successfully then the checkdeps output will end with SUCCESS for each check. An example of the sort of output you should expect from a successful installation is: checkdeps-log-success.txt .

  • Once you have achieved SUCCESS then run checkdeps on the other hosts that you want to run the software on.

  • In addition run checkdeps from a normal users account to make sure there are no permissions issues.

  • If you have time and are interested then you could conduct more thorough checks involving running individual programs:

8. BUSTER user access

  • For users to run programs from the BUSTER suite they need to invoke our setup script.

  • A good way to do this is to create a soft link called BUSTER_latest to the directory for the installation we have just made:

cd ~/GPhL
rm -f BUSTER_latest
ln -s BUSTER_snapshot_20240123 BUSTER_latest

  • The soft link is useful because it means that when in the future you install a new version of the software the soft link can be updated so that users automatically use the latest version of the software (but the previous version will still be available if wanted).

  • Once you have created the soft link, bash, dash & zsh users should access the software typically by adding the following lines to their ~/.bashrc file:

# Provide access to BUSTER package (refine, grade2, aB_autorefine, rhofit, pipedream …):
. ~software/GPhL/BUSTER_latest/setup.sh

  • csh or tcsh users should access the software typically by adding the following lines to their ~/.cshrc file:

# Provide access to BUSTER package (refine, grade2, aB_autorefine, rhofit, pipedream …):
source ~software/GPhL/BUSTER_latest/setup.csh

  • In addition, the BUSTER tools visualise-geometry-coot and visualise-rhofit-coot require that coot is on the user’s PATH. The standard CCP4 (version 6.5 or later) setup scripts now provide for this.

  • You may also want to provide user access to directly run the other software (for instance mogul) but this is not necessary to run BUSTER tools.

  • If you have a site-specific special mechanism to provide access to software then this should be used instead!

  • Reference cards that provide users with a summary of the most useful tools and options are supplied in the installation. It can be useful if these can be printed (double sided) and supplied to users. Or you might want to include their location in an announcement email. The reference cards can be found: