Running PHENIX under Windows via a Virtual Machine running Linux

Mike Blaber 08/22/10


I wanted to try to run PHENIX (Linux-based) under Windows.  There were three different Virtual Machine (VM) programs I tried: 1) Oracle VM Virtual Box, 2) Micosoft Virtual PC 2007 and 3) VMware Player.  I initially worked with Oracle VM Virtual Box.  It installed and I was able to run and load CCP4, COOT and PHENIX.  These programs worked on the VM; however, the COOT window was infrequently updated and had issues with incorrectly displaying menu items, etc., due to this issue.  I was working around the problem by using a working directory that was a shared folder between the Linux and Windows OS’s, then running COOT under Windows.  This was O.K., but I decided to try other VM programs to see if the problem was universal.  Next I tried Microsoft’s Virtual PC 2007 (this is for non Windows 7 computers).  I had problems in installing a VM with this program; also, the control of the mouse pointer was awkward (the mouse pointer was not released from the Linux window unless you used a particular key-stroke combination). Then I tried VMware Player and this seemed to have the fewest problems, and also displayed and updated the COOT window correctly under Linux.  Here is the installation process I followed (using Ubuntu 10.04 version of Linux):


Procedure (Note: all software is free)

1.    Download Ubuntu ( (free Linux operating system)

a.    This will be an "ISO" file that you need to burn to disk (CD)

b.    Ubuntu 10.04 was the version I used (8/22/10)

c.    Download InfraRecorder (free) to enable burning of ISO files (

d.    Burn Ubuntu onto CDROM using the installed InfraRecorder software

2.    Download free VMware Player software at

3.    Install

a.    Put the Ubuntu diskette into the CDROM

b.    Create a new virtual machine

c.    Select the CDROM that will load the Ubuntu OS (should be automatically detected)

d.    Should say Ubuntu detected and "this operating system will use Easy Install"

e.    Enter full name, user name, and password

f.     Select virtual machine name and location (note: location should be on the local machine and not a network drive – too slow otherwise)

g.    Select max disk size of 100 GB

h.    Store virtual disk as single file

i.      Customize hardware:

                                          i.    Memory size (1.5 GB)

                                        ii.    Processor cores (2)

                                       iii.    Display – accelerate 3D graphics

j.      Power on virtual machine after creation

k.    Finish

4.    First time power up

a.    Ubuntu installs. VM reboots

b.    VMware Tools should install automatically (provides capability for shared folders, and installs a SVGA driver for improved video performance).  The installation screen pauses and states the VMware Tools are being installed.  This package can be installed later if it is not installed now (it is installed as part of the "Easy Install" process)

c.    Ubuntu login window appears.  Login with the password you set up earlier.

d.    Check the time (upper right).  Click "Locations" then edit if the time is incorrect

e.    Lower left may indicate update manager has updated files to install.  Click & update files as necessary.

                                          i.    Note: had some issue about installing "Grub", but chose option to continue without installation of this package

f.     Shut down the Linux VM

5.    Setting up shared folders

a.    Create a folder in Windows (e.g. C:\windbuntu)

                                          i.    Permit sharing permission on this folder

b.    Start VMware Player

c.    Select Ubuntu VM (don’t start it though)

d.    Select "Options" tab

                                          i.    Click on "Shared folders"

                                        ii.    Click on "Always enable" on the folder sharing window on the right

                                       iii.    Add the path to the shared folder on Windows (e.g. C:\winbuntu)

                                       iv.    Click next, click "enable this share". Click finish

e.    Start the Linux VM

f.     Note: the shared folder should be in /mnt/hgfs

g.    If the shared folder is not visible, maybe the VMware Tools was not installed (or it was an old version).  Click Virtual Machine at very top of window. Select "Reinstall VMware Tools…"

                                          i.    A file browser will open up with a compressed file (VMwareTools-8.4.3-282343.tar.gz).  Right click, select "open with archive manager"

                                        ii.    Click extract (to folder where you have permission; e.g. create folder:  /user-name/temp)

                                       iii.    Open terminal window; go to the folder you extracted the files to. Type $ sudo ./

                                       iv.    Restart system after installation

h.    Now go to /mnt/hgfs and confirm that the shared folder is visible

i.      Note: if you open a file browser and drag this folder icon to the left menu, it will be accessible when you click on "Places" tab on the top of the window

6.    CCP4 (NOTE: install CCP4, then COOT, then PHENIX in this order)

a.    Download the CCP4 suite of programs (enables modeling within PHENIX and modeling with COOT) free from

b.    Note: you can either do this from Windows and save into the winbuntu folder (visible to Ubuntu) or download from within Ubuntu (either way, download the Linux version)

c.    Right click the file and select "open with archive manager"

d.    Extract all files

e.    Suggest making a folder /home/user-name/data/ccp4 and either copying or extracting the files to this folder (where user-name is your user name)

f.     Open a terminal window and go to /home/user-name/data/ccp4

g.    Then type:

$  ./

h.    Select location to install (accept default since you have write privileges in this folder)

i.      The installation offers to modify the environment variables to enable running without having to (re)source the environment variables.  Do this.

j.      Open a new terminal window and type "ccp4i"; the CCP4 program should run

7.    COOT

a.    Although the CCP4 package is supposed to include COOT it doesn’t seem to install a functioning version, so download appropriate OS version free from

b.    For Ubuntu I tried binary-Linux-i686-ubuntu-8.04.4-python-gtk2  (this worked)

c.    Make a directory /home/user-name/data/coot and extract to this folder

d.    Edit /home/user-name/data/ccp4/setup-scripts/sh/ccp4-others.setup to change the directory that the coot executable is now in (after installing the i686 Ubuntu version).  This appears to be sourced upon opening a terminal window

                                          i.    Open a terminal window and type
$ which coot

                                        ii.    This should show the correct executable directory

                                       iii.    Type $ coot to try it out (should execute coot)

8.    PHENIX

a.    Request a free download password from

b.    Make directory "phenix" from the "data" directory.

c.    Extract then install to this directory

d.    Open terminal window, go to the /data/phenix/phenix-installer-1.6.4-486 directory

e.    Type $ sudo ./install (this will install in /usr/local/ which requires sudo permission)

f.     Set up sourcing of phenix location by editing the previously edited ccp4 script:

g.    $ gedit /home/user-name/data/ccp4/setup-scripts/sh/ccp4-others.setup

h.    Add ".  /usr/local/phenix-1.6.4-486/" at the end

i.      Open a new terminal window and start PHENIX by typing $ phenix

9.    Everything should work now. Opening a terminal window and typing $ phenix will start PHENIX and COOT should load during refinement

10. NOTE: Phenix uses csh/tcsh commands when running the OMIT MAP wizard (and possibly other routines).  To install csh/tcsh type:
$ sudo apt-get update
$ sudo apt-get install csh