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Subsections
Referencing SSRL
The following statement should be included in the acknowledgement
section of publications that are based in part or fully on data
collected at the macromolecular crystallography beamlines:
"Portions of this research were carried out at the Stanford
Synchrotron Radiation Laboratory, a national user facility operated by
Stanford University on behalf of the U.S. Department of Energy, Office
of Basic Energy Sciences. The SSRL Structural Molecular Biology
Program is supported by the Department of Energy, Office of Biological
and Environmental Research, and by the National Institutes of Health,
National Center for Research Resources, Biomedical Technology Program,
and the National Institute of General Medical Sciences."
You are also encouraged to acknowledge your support staff contact person
if they provide help during your beamtime. If the support staff make
particularly valuable suggestions or contribute in a non negligible
way to the sucess of the experiment, you may consider making them
coauthors in resulting publications.
It is very important that you tell us about publications relevant to
work conducted at SSRL. Please fill out
the publication
form.
References to supported software/hardware
The following are references of supported software/hardware at
the SSRL. Please use the appropriate references in your publications.
Data collection
Blu-Ice: McPhillips, T. M., McPhillips, S. E., Chiu, H. J., Cohen,
A. E., Deacon, A. M., Ellis, P. J., Garman, E., Gonzalez, A., Sauter, N. K.,
Phizackerley, R. P., Soltis, S. M., Kuhn, P. Blu-Ice and the Distributed
Control System: software for data acquisition and instrument control
at macromolecular crystallography beamlines. (2002) J. Synchrotron
Rad. 9, 401-406.
Automated sample mounting system: Cohen, A. E., Ellis, P. J.,
Miller, M. D., Deacon, A. M. and Phizackerley, R. P. An automated system
to mount cryo-cooled protein crystals on a synchrotron beamline, using
compact sample cassettes and a small-scale robot. (2002) J. Appl.
Cryst. 35, 720-726.
Fluorescence scan analysis: Evans G., Pettifer
R. F. CHOOCH: a program for deriving anomalous- scattering factors
from X-ray fluorescence spectra. (2001) J. Appl. Cryst.
34, 82-86.
http://www.gwyndafevans.co.uk/chooch.html
Derivative preparation with SSRL Xe-Kr cell: Cohen, A., Ellis,
P., Kresge, N. & Soltis, S. M. MAD phasing with krypton. (2001)
Acta Cryst. D57, 233-238.
Data analysis with Web-Ice
Web-Ice: Gonzalez, A., Moorhead, P., McPhillips, S. E.,
Song, J., Sharp, K., Taylor, J. R., Adams, P. D., Sauter, N. K. &
Soltis, S. M. Web-Ice: Integrated Data Collection and Analysis
for Macromolecular Crystallography. (2008) J. Appl. Cryst. 41, 176-184.
Mosflm: Leslie, A. G. Integration of macromolecular diffraction
data. (1999) Acta Cryst. D55, 1696-1702.
Labelit: Sauter, N. K., Grosse-Kunstleve, R. W. &
Adams. J. Appl. Cryst. 2004 37:399-409.
Spotfinder/DISTIL: Zhang, Z., van den Bedem, H., Sauter,
N. K., Snell, G. & Deacon, A. Automated diffraction image analysis and
spot searching for high-throughput crystal screening. (2006)
J. Appl. Cryst. 39, 112-119.
Data processing with SSRL scripts (mosflm, scale and MAD
scripts)
Mosflm, Scala, Truncate, Scaleit, fft: Collaborative
Computational Project, Number 4. The CCP4 Suite: Programs for Protein
Crystallography. (1994) Acta Cryst. D50, 760-763.
Mosflm: Leslie, A. G. Integration of macromolecular diffraction
data. (1999) Acta Cryst. D55, 1696-1702.
Mosflm (autoindexing): Powell, H. R. The Rossmann Fourier
autoindexing algorithm in MOSFLM. (1999) Acta Cryst. D
55, 1690-1695.
Solve: Terwilliger, T. C., Berendzen J. Automated
MAD and MIR structure solution. (1999) Acta Cryst. D55,
849-861.
Resolve (density modification): Terwilliger, T. C. Maximum
likelihood density modification (2000) Acta Cryst. D
56, 965-972.
Resolve (model-building): Terwilliger, T. C. Automated main-chain
model-building by template-matching and iterative fragment
extension. (2003) Acta Cryst. D59, 38-44.
http://www.solve.lanl.gov/
Shelxd: Schneider, T. R. & Sheldrick, G. M. Substructure
solution with SHELXD. (2002) Acta Cryst. D58, 1772-1779.
Shelxe: Sheldrick, G. M. Macromolecular phasing with
SHELXE. (2002) Z. Kristallogr. 217, 644-650.
Anything that starts with shelx...: Sheldrick, G. M. A short
history of SHELX (2008). Acta Cryst. A64, 112-122.
http://shelx.uni-ac.gwdg.de/SHELX/
Data processing with HKL2000
Otwinowski, Z., Minor, W. Processing of X-ray diffraction data collected
in oscillation mode. (1997) Methods Enzymol. 276, 307-326.
http://www.hkl-xray.com/
Data processing with XDS
Kabsch, W. Automatic processing of rotation diffraction data from
crystals of initially unknown symmetry and cell constants. (1993)
J. Appl. Cryst. 26, 795-800.
Graphics software
Coot:
Emsley, P. and Cowtan, K. Coot: Model-Building Tools for Molecular
Graphics. (2004) Acta Cryst. D60, 2126-2132.
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