CCP14 Homepage - Single Crystal and Powder Diffraction - Methods, Problems and Solutions - CCD Control and CCD Processing Software for Crystallography

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CCP14

Methods, Problems and Solutions

CCD Control and CCD Processing Software for Crystallography

The CCP14 Homepage is at http://www.ccp14.ac.uk

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[Software for Integrating Intensities From Image Plates]

Known Available Software (or software still being chased):

Additions/Corrections/Changes Welcome

The Post to sci.techniques.xtallography and bionet.xtallography

From: l.cranswick@dl.ac.uk (Lachlan Cranswick) Newsgroups: sci.techniques.xtallography,bionet.xtallography Subject: Available software to control and collect CCD single crystal data? Date: Mon, 17 Apr 2000 16:47:35 LOCAL Organization: CCP14 Project, Daresbury Laboratory, UK From the recent British Crystallographic Association conference in Edinburgh, the most commong type of software request that stood out the most: "Is there software in the public domain which will massage CCD single crystal data (i.e. find the unit cell, index reflections, determine their intensities)" (The emphasis was on small molecules but would people be able to post/pass on relevant links relating to CCD software for Protein and small molecule work? ) Including: Public Domain software and Commercial software Thanks in advance (will summarize if get some hits on this), Lachlan. ====================== Lachlan M. D. Cranswick Collaborative Computational Project No 14 (CCP14) for Single Crystal and Powder Diffraction Daresbury Laboratory, Warrington, WA4 4AD U.K Tel: +44-1925-603703 Fax: +44-1925-603124 E-mail: l.cranswick@dl.ac.uk Ext: 3703 Room C14 http://www.ccp14.ac.uk

ADSC/Cornell/Purdue graphical user interface to DPS/Mosflm/CCP4 data processing

"The working routines include":
- DPS indexing - autoindexing of one or more oscillation images, by Ingo Stellar of Michael Rossmann's group at Purdue.
- mosflm - general program for refinement and integration of images, by Andrew Leslie of the MRC. Also can be used for indexing.
- postchk - refinement of cell parameters. This program was formerly part of the CCP4 suite; it is no longer supplied with CCP4 but can still be useful for processing macromolecular data.
- CCP4 routines - the programs sortmtz, scala, and truncate are used for sorting, scaling, merging, and producing the final output. These are the standard versions from CCP4.
- DPS scaling - an alternative to scala, developed at Purdue.
ADSC webpage:
http://www.chess.cornell.edu/MacCHESS/processing_gui.html
DPS webpage:
http://ultdev.chess.cornell.edu/MacCHESS/DPS/
Michael G. Rossmann webpage:
http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/
(Refer: i) Rossmann, M. G., C. G. van Beek. 1999. Data processing. Acta Crystallogr. D55:1631-1640; ii) Bolotovsky, R., I. Steller, M. G. Rossmann. 1998. The use of partial reflections for scaling and averaging Xray area-detector data. J. Appl. Crystallogr. 31:708-717; and iii) Steller, I., R. Bolotovsky, M. G. Rossmann. 1997. An algorithm for automatic indexing of oscillation images using Fourier analysis. J. Appl. Crystallogr. 30:1036-1040. )
Download site: ftp://bridgedec.chess.cornell.edu

d*TREK and CrystalClear by MSC (Molecular Structure Corporation)

MSC (Molecular Structure Corporation): http://www.msc.com/.
d*TREK (A Universal Data Processing Package for IP and CCD Detectors): http://www.msc.com/smc/dtrek.html.
CrystalClear for Windows (Area detector control and data processing): http://www.msc.com/smc/cc.html.

DENZO/HKL

"The HKL suite is a package of programs intended for the analysis of X-ray diffraction data collected from single crystals."
DENZO/HKL webpage:
http://www.hkl-xray.com/.
DENZO/HK License Policy for either non-profit or commercial users:
http://www.hkl-xray.com/license_policy.htm.
DENZO/HK Software Download Instructions:
http://www.hkl-xray.com/download_ftp.htm.
The programs have been written by Dr. Zbyszek Otwinowski (Southwestern Medical Center, University of Texas) and Dr. Wladek Minor (University of Virginia):
- Dr. Zbyszek Otwinowski: http://www.swmed.edu/home_pages/grad/webrib/otwinows.htm.
- Dr. Wladek Minor: http://olenka.med.virginia.edu/newcsb2/wladek.html.
DENZO/HKL - program suite for oscillation data processing :
- http://www.x12c.nsls.bnl.gov/x12c/hkl_banner.html.
- DENZO - Auto-indexing, refinement and integration
- XDISPLAYF - Image display and measurement
- SCALEPACK - Data scaling

Gzwilling - Ralf Muller

Contact: ralf@deres-mueller.de
WEB SITE
Matrix free integration of image plate and CCD single crystal diffraction data for Linux (released under the GPL and under development)
Original at http://www.deres-mueller.de/gzwilling/
[CCP14 UK Web Mirror] | [Canadian CCP14 Mirror] | [US CCP14 Mirror] | [Australian CCP14 Mirror]

JITAX (GPL'd) - by Scott Belmonte

Freely available as C source code under the GNU Public Licence
"JITAX - Some experimental/example source code for the processing of Bruker SMART CCD Frames (and any other type of CCD Data you define in the code)."
Some applications code include:
- reading and writing Bruker CCD frame files (and writing out PNG format files as well)
- mask.c - Masking nasty parts of frames to help with indexing and integration.
- subtract.c - Background subtraction (powder rings and other nasties)
- jitax.c - Background subtraction with running average options for the "standard frame".
- (command line options to output to PNG format files with contrast options)
Download: [CCP14 UK Web Mirror] | [Canadian CCP14 Mirror] | [US CCP14 Mirror] | [Australian CCP14 Mirror]

JITAX 77 (GPL'd) - by Scott Belmonte (for Stanley Nyburg)

Freely available as Fortran 77 source code under the GNU Public Licence
Jitax 77 will perform:
- read in Photonics Science CCD TIF files and output FLF format files
- background subtraction from a reference "no sample" frame
- merging of frames
- cosmic ray correction (using a minimum function)
- and dynamically determined (minimum function) background correction (as well as a few other options)
Download: [CCP14 UK Web Mirror] | [Canadian CCP14 Mirror] | [US CCP14 Mirror] | [Australian CCP14 Mirror]

MOSFLM (The program is free to both academics and industry) (Andrew Leslie et al)

Refer Harry Powell webpage:
- http://www.mrc-lmb.cam.ac.uk/harry/.
- MOSFLM Homepage: http://www.mrc-lmb.cam.ac.uk/harry/mosflm/.
- Download site: ftp://ftp.mrc-lmb.cam.ac.uk/pub/mosflm/.
- "If you want to process images with plenty of spots (say, >200 per image) which are a mixture of fullies and partials, I'd try MOSFLM (see my web-pages at http://www.mrc-lmb.cam.ac.uk/harry); we do have _some_ CCDs included in our setup (ADSC, Mar CCD), but users can easily (!) add their own, and if there's a perceived demand we will add them to the types supported by default.
  If you routinely do fine phi slicing (so that you don't have any fullies) I'd recommend trying XDS (from Wolfgang Kabsch, sorry, I can't remember the URL) or d*Trek (from Jim Pflugrath of MSC, but I believe that costs after a trial period)."
MOSFLM 6.0 User Guide (This describes MOSFLM version 6 for processing image plate and CCD data): http://www.mrc-lmb.cam.ac.uk/harry/mosflm/mosflm_user_guide.html.
Mosflm version 5.4 - User guide (This describes MOSFLM version 5.40 for processing image plate data): http://bio5.chemie.uni-freiburg.de/~maveyrau/manuals/mosflm_user_guide.html.
Refer: EMBL Hamburg practical PX course 1999 : http://www.embl-hamburg.de/ExternalInfo/px99/speakers.html.

PUXTAL (The Purdue University XTAL Programs Library)

Downloadable tar.gz program files and examples.
PUXTAL webpage:
http://www-structure.bio.purdue.edu/~kvz/.
Data Processing Programs (SCANDUMP, OSC123, MGROSC, COMBINE, MGRSC, UNIVERSE):
http://www-structure.bio.purdue.edu/~kvz/#DATAPROC.

"Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement,"

Homepage: http://www.x12c.nsls.bnl.gov/rr_course/.
Agenda: http://www.x12c.nsls.bnl.gov/rr_course/course_agenda.html.

XDS (from Wolfgang Kabsch)

X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method.
XDS is free of charge for non-commercial applications; a license is required for industrial usage (e-mail enquiry to : Wolfgang.Kabsch@mpimf-heidelberg.mpg.de).
- XDS Homepage: http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/
- Executables in the package:
  - xdsman - Shell-script that provides the xds manuals.Calling xdsman, the user may select the manual he wants to see.
  - xdstemplate - Shell-script that provides templates for XDS input files in the user's selected data processing directory.
  - xds - Main data processing program for rotation images. A program description is given in file 'xds.man'.
  - xscale - Scaling program for xds-produced data sets. A program description is given in file 'xscale.man'.
  - xdsconv - Converts reflection intensities as generated by xds to amplitudes in a format suitable for CNS and other structure solution program packages. A program description is given in file 'xdsconv.man'.
  - xplan - Program to help planning data collection. A program description is given in file 'xplan.man'.
  - VIEW - Program to look at images (Author W.Gebhard). Type VIEW -h to get a program description.
  - cellparm - Estimates cell constants from a number of XDS-runs. A program description is given in file 'cellparm.man'.
  - xspot - Interactive program to extract strong diffraction spots from file PROFIT.HKL for use in the IDXREF step.
  - 2pck - Converts detector images into files of type CCP4, compressed by J.P.Abraham's algorithm. The converted (and compressed) images are acceptable to xds. A program description is given in file '2pck.man'.

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