User Guide – Crystallography Software

Page Contents

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
Data Processing
Autoprocess autoprocess any_frame
XDS xds
Mosflm imosflm
xia2 xia2 /directory_where_images_are
HKL2000 not supported, site files available below
Data Analysis
PHENIX phenix
Solve/Resolve phenix or (various)
CCP4 ccp4i
SHELX ccp4i or (various)
ARP/wARP ccp4i or (various)
CNS (various)
XPREP xprep
AutoPartha runPartha
Model Building
Coot coot
PyMOL pymol

Data Processing

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.

Mosflm

imosflm

xia2

xia2 [options] [/directory/where/images/are]

HKL2000

  • 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):
    • 08ID-300 for the MarCCD 300 currently in use at beamline 08ID-1
    • 08ID-225 for the MarCCD 225 which was in use at beamline 08ID-1 before April 2010
    • 08B1-300HE for the MarCCD 300HE currently in use at beamline 08B1-1

Data Analysis

PHENIX

phenix

CCP4

ccp4i

SHELX

ccp4i

You may also wish to make use of the hkl2map application

hkl2map

CNS

Solve/Resolve

 ARP/wARP

ccp4i

XPREP

xprep

AutoPartha

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
runPartha

Model Building

Coot

coot

PyMOL 

pymol