1. Stony Brook Integrative Structural Biology Organization
Introduction to Linux and Crystallography Software
September 17, 2016
LSB 434

2. Outline I. Linux What is Linux Linux Distributions
Desktop Environments
Command-Line
II. Crystallography
Image Analysis
Solution Analysis

3. What is Linux Linux is a UNIX-like open-source operating system
Linux kernel was created by Linus Torvalds in 1991
Android OS is based on linux kernel
Internet runs on linux
Most servers run linux

4. Linux Distributions (Distros)
Linux is usually packaged into distributions
Ubuntu (Debian based)
Debian
Fedora/Red Hat Enterprise Linux (RHEL)
OpenSUSE/SUSE Enterprise Linux (SEL)
Linux Mint (Ubuntu based)
CentOS (Derived from RHEL)
Scientific Linux (Derived from RHEL)

5. How do you get a pretty interface

6. Desktop Environments
Unity, KDE, GNOME, Cinnamon, XFCE, MATE, LXDE

7. Terminal or Command Line Interface
Shell is a command-line interpreter
BASH (Bourne-Again Shell)6
C-Shell
tcsh

8. Applications
Applications can be downloaded from repositories (like an app store)
Thousands of software packages available
Free and Open Source Software (FOSS)

9. Package Managers YUM- .RPM APT- .DEB
RPM Distros (RHEL, Fedora, SEL, CentOS)
APT- .DEB
DEB Distros (anything derived from Debian, e.g. Ubuntu)

10. X-Ray Crystallography

11. X-ray Crystallography Initial Analysis
Common Applications
HKL2000/3000
XDS
iMosfilm/Pointless/Aimless

12. Structure Analysis
Collaborative Computational Project No. 4 (CCP4)
Suite of separate programs
Can start from raw images
Integration with other programs (SHELX, ARP/WARP)
Started in 1979
Multiplatform (Windows, MacOS, Linux)
Phenix (Python-based Hierarchical Environment for Integrated Xtallography)
Integrated suite of programs
Requires processed file
Advanced GUI
Available 2002
MacOS and Linux (limited support for windows)

13. Hands-on Part

14. Download Ubuntu Server 16.04.1 LTS Download VirtualBox

41. LVM-logical
Volume management

56. Install Synaptic Package Manager

63. CCP4 Installation Sudo chown roger /opt Run ccp4 setup file
Source /opt/ccp4-7.0/bin
Refresh . ~/.bashrc

64. Phenix Installation Cd Downloads ./install –prefix=/opt/phenix
Source env.sh
Refresh . ~/.bashrc

65. XDS Installation Extract XDS to /opt Rename xds gui download to xdsgui
Move xdsgui and xds-viewer to /opt
Change permission xdsgui to allow execution as program
Sudo ln –s /usr/lib/x86_64-linux-gnu/libmng.so.2 /usr/lib/x86_64-linux-gnu/libmng.so.1
apt-get install libatk-adaptor libgail-common
export PATH=“/opt:”$PATH
export PATH=“/opt/xds:”$PATH
export KMP_STACKSIZE=8m