Crystallographic Computing - Basic Linux /Unix
In-house Info - Mac Info and Resources - Pymol Resources

Crystallographic Computing

Given that a large portion of the work involved in solving a crystal structure involves computatuional analysys of your data, it is a good idea to become as profecient as possible on a Linux/Unix workstation. I really feel that the best way to acomplish this is to sit down in fromt of the workstation and fiddle around, get to know the commands with a UNIX book from the library and play. The system is protected from general users so you can't hurt anything. So go on, open a terminal window, don't be afraid. Use the links below to access Linux/UNIX resources (all of those commands work at the Mac command line too!!) and use these links to learn the crystallography software to analyze your beautiful data!

HKL Research
CCP4
Solve/Resolve
Sharp
SnB
CNS

Basic Linux / Unix

Volumes have been written on how to master linux, learn it in 24 hrs, run your own webserver for fun and profit, etc, etc. All we present here is links that have been helpful to us. Below are links to the linux distributions used in the lab, documentation and support sites. The greatest part of the linux community is the support system so if you have a problem, Google it. Its likely that someone has an answer.

Red Hat Linux
Gentoo Linux
Linuxquestions.org
The linux documentation project
Kernel.org
Apache web server
SGI / IRIX

 

Mac Info and Resources

With the introduction of Os X Apple has been embraced by all of the old biologists / techies that grew up with Apples. In short, thanks to the BSD subsystem that Os X is built on it possible to port ANY application that runs on a *NIX platform to the Mac, wow. This is of course great for anyone running a lab that requires UNIX enabled computational work, now we can buy one macine to analyze our data with UNIX programs and use that same machine to write up our results using familiar programs such as Microsoft Word and the Adobe family of software. Most crystallography applicatons have been ported to Os X, including builders such as O and Turbo Frodo. Below are links to relevant mac sites and tips for suing your mac for all of your UNIX / crystallography needs.

Apple's Website
Mac OsX Hints
Fink
PPC Linux
Dr. William Scott's Page for Crystallography on OsX
Darwin Ports
Macrumors.com

Pymol Tutorials and Tips

Pymol is a fantastic molecular modeling program available for many computing platforms. It has a intuative WYSIWYG interface and a nice ray tracing engine makin very nice pictures a breeze. Its also easily scriptible, making complex tasks and movies easy. Here are some helpful pymol links and some tutorials of our own to get you started.

Pymol main page
Pymol mail lists
Robert Campbell's collection of scripts

Tutorials

Select, display, render and export
Density maps and Denisty map pictures
Adjust clip and slab for perfect images
Export to povray
Tips and tricks for Display

In House Computing Info

Here is where I plan to put the info for the lab network. What programs are on what machines, what IP goes where, etc. Of course all of these goodies will be password restricted. And I need the machines before I complete this section... all in good time.