User Guide – Crystallography Software

Page Contents

The CMCF supports a variety of data processing, data analysis, and model building programs. These programs can be run from a local terminal from any user workstation at the beamline or NX session. Some programs can also be run on our high-capacity data processing servers for fastest data processing.

The following sections detail the programs available to academic users, and how best to run each program.

Program Name Startup Command
Data Processing -- run from data processing server
Autoprocess autoprocess any_frame
XDS xds
Mosflm imosflm
xia2 xia2 /directory_where_images_are
HKL2000 not supported, site files available below
Data Analysis -- run from data processing server or local terminal
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 -- run from local terminal
Coot coot
PyMOL pymol
Chemical Crystallography
mosgo (strategy determination) msg
xdsgo (data processing) xdsgo
sms (structure solution) sms

Data Processing

The CMCF has high-capacity data processing servers dedicated to serve users. Whenever possible, use a data processing console for fastest data processing using the following programs.
To access these servers, open a Data Processing console by clicking on the icon on the Desktop of the user workstation at the beamline or NX session.

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 which was in use at beamline 08ID-1 April 2010 - February 2017
    • 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

The following data analysis programs can either be run through a local terminal or in a Data Processing console (accessed by clicking on the icon on the desktop of the user workstation at the beamline or NX session).  In some cases, speed will be improved by running in a data processing console, but some features of these programs are only accessible locally (for example, model building with Phenix).

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

The following model building programs are graphics applications that should be run from a local terminal on a user workstation at the beamline or NX session. Note: These applications are not available from the data processing servers.

Coot

coot

PyMOL 

pymol

 

Chemical Crystallography

MSG

MSG (Mosflm-Go) is a strategy determination program developed at CMCF. MSG uses Mosflm for cell indexing and strategy determination. To invoke MSG, type:

Examples:

running msg with a specific frame name:

msg frame_name

to enforce a specific space group:

msg frame_name -s 19 (or P212121)

to access recently collected frames in MxDC:

msg -x

to change default oscillation angle for strategy determination:

msg frame_name -o 0.2

to access recently created frames via lsl:

lsl -m(works best in subdirectories)

All the above options could also be accessed with lsl. For example, to calculate a data collection strategy with the last created frames, specific space group, and oscillation angle type:

lsl -m -s 19 -o 0.5

Example of output:

Please cite mosflm in your publications: T.G.G. Battye, L. Kontogiannis, O. Johnson, H.R. Powell and A.G.W. Leslie 2011, Acta Cryst. D67, 271-281.

 

XDSGO

XDSGO is a data reduction program, which was developed at CMCF. It utilises the XDS package for data reduction and Sadabs program for data correction and merging. To invoke XDSGO, navigate to your data folder and type:

xdsgo

To integrate multiple datasets the following command can be used:

xdsgo -m /path/to/first/data_directory /path/to/second/data_directory  /path/to/N/data_directory

XDSGO creates input files for XDS, XSCALE, and SADABS and run those programs in sequence. Data conversion between XDS file format and SADABS file format is accomplished via the XDS2SAD program. XDSGO is designed to recover from all the posible errors and usualy does not require user input. It creates standard XDS output files and provides a data statistics report in html format. All the above mentioned files can be found in the "proc" direcotry created in the dataset directory from which it is run.

Example of data processing:

 

SMS

SMS is a structure solution program. It utilizes XPREP and SHELXT for data solution. It supports XDS, Scalepack, and shelx input file formats, and outputs the solution in a shelx compatible format. To invoke sms, navigate to your "proc" folder, created by XDSGO, and type:

sms -xds XDS_ASCII.HKL -f FORMULA -o OUTPUT_FILE_NAME

Both XDSGO and SMS can be run in sequence from your data directory using the following command:

sms -a -f FORMULA -o OUTPUT_FILENAME

Other SMS options can be accessed by typing:

sms -h

which will result in the following output:

-h        Print this help message
-o        Output file name
-xds      XDS input file
-sca      Scalepack input file
-sx       Shelx input file
-f        Formula
-c        Cell parameters (required by shelx file format)
-w        Wavelength in Angstrom
-a        Automatic data reduction (XDS), scaling (SADABS) and solution (SHELXT
References
1) Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 1993, 26, 795-800.
2) Sheldrick, G. M. Sadabs; University of Gottingen, Germany Program for Empirical Absorption Correction of Area Detector Data, 1996.
3) Sheldrick, G. M. 2008 XDS2SAD. University of Gottingen, Germany
4) XPREP 2014; X-ray data Preparation and Reciprocal space Exploration Program.Bruker AXS Inc., Madison, Wisconsin, USA.