User Guide – Crystallography Software
The CMCF has high-capacity data processing servers dedicated to serve users. To access these servers for use with most of the programs listed below, open a Data Processing console by clicking on the icon on the Desktop of the beamline computer terminal. Use the Data Processing console whenever possible for fastest data processing.
Note that HKL2000 must be run on a specific server which is accessed by clicking on the HKL2000 icon on the Desktop.
The following programs are available at the CMCF for academic users. Note that some programs are only available through a remote session on the Data Processing server.
|Program Name||Startup Command|
|HKL2000||not supported, site files available below|
|Solve/Resolve||phenix or (various)|
|SHELX||ccp4i or (various)|
|ARP/wARP||ccp4i or (various)|
XDS & Autoprocess
Using XDS is made easy at the CMCF through an in-house script called Autoprocess which generates the appropriate input files and runs XDS automatically. You can also use XDS in the traditional manner. We recommend running Autoprocess to generate the appropriate input files which you can then edit manually.
- xia2 homepage & manual
- xia2 is run by typing
xia2 [options] [/directory/where/images/are]
- HKL2000 is not supported at this time
- Running HKL2000 off-site with data collected at CMCF will require a site file corresponding to one of the following detectors (click to download site file):
- CCP4 homepage & manual
- Start the CCP4 graphical user interface by typing
You may also wish to make use of the hkl2map application
- ARP/wARP homepage
- run ARP/wARP in the CCP4 graphical user interface by typing
- XPREP tutorial
- XPREP is available by typing
Partha is a program develloped by Peter Zwart [Acta Cryst. (2005) D61, 1437-1448] that simulates SAD data and estimates the likelihood of success of SAD phasing, given a set of parameters. "AutoPartha" is an application for using Partha, developed and adapted for use at the CMCF. It includes easily accessible choices of energies available at the facility, automatic calculations of theoretical f' and f" and an adaptive scoring mechanism based on the literature and experience.
- AutoPartha is invoked by typing
- Coot homepage
- start Coot by typing
- PyMOL homepage
- start PyMOL by typing