Cryo-EM Modeling Based on X-ray Crystallography Workshop, Urbana, Jan. 8-10, 2014
Laptop Setup
This page describes how workshop participants should set up their laptops for participation in workshop hands-on tutorial sessions.
I. Install Software
Tutorial sessions use the VMD - version 1.9.1 and NAMD - version 2.9 software packages, plus plotting programs (e.g., Excel on Windows, XMGrace on Unix/Mac) and text editors (e.g, Notepad on Windows, Emacs, vi on Unix, TextEdit on Mac) as described on the laptop requirements page. Be sure that all your software is installed and tested before you arrive at the workshop - there is no time on site for installation troubleshooting.
The program DireX (Version 0.6.2) must be installed for the DireX tutorial. Note: a Windows version of DireX is not currently available; participants will be directed to TCBG Linux machines as needed to complete the tutorial.
II. Install Tutorial Texts and Files
Each tutorial consists of a text in pdf format, and computer files used in the tutorial. Be sure that you have the files you need each day of the tutorial sessions in place before you arrive at the workshop. Files by day of workshop tutorial session are listed below. It is easiest to follow the tutorials if files are placed in a 'Workshop' directory on the desktop.
Day 1 - Principles and Applications of Molecular Dynamics Flexible Fitting - Klaus Schulten and TCBG Members
- Using VMD:
(pdf, 1.6M) (required tutorial files [.tar.gz, 44.9M], [.zip, 44.9M], Individual files) - NAMD Tutorial:
pdf for Unix/Mac, or pdf for Windows
required tutorial files (all platforms) [.tar.gz, 148M], [.zip, 148M], individual files (all platforms)
Day 2: Structural Modeling Using DireX and DEN - Gunnar Schroeder
- DireX Tutorial:
(pdf, 5.7M) (required tutorial files [.tar.gz, 20.1M]) - MDFF Tutorial:
(pdf, 1.3M ) (required tutorial files [.tar.gz, 98.2M], [.zip, 98.2M], individual files) - Structure Check Tutorial:
(pdf, 720k ) (required tutorial files [.tar.gz, 762k], [.zip, 753k], individual files)
