Cite
=========

RAW
----

If you use RAW in your research, please cite the newest RAW paper:

*BioXTAS RAW 2: new developments for a free open-source program for
small-angle scattering data reduction and analysis.* J. B. Hopkins.
Journal of Applied Crystallography (2024), 57, 194-208.

DOI: `10.1107/S1600576723011019 <https://doi.org/10.1107/S1600576723011019>`_


You can also cite the previous RAW papers if you like:

*BioXTAS RAW: improvements to a free open-source program for small-angle X-ray
scattering data reduction and analysis.* J. B. Hopkins, R. E. Gillilan, and S. Skou.
Journal of Applied Crystallography (2017), 50, 1545-1553.

DOI: `10.1107/S1600576717011438 <https://doi.org/10.1107/S1600576717011438>`_

*BioXTAS RAW, a software program for high-throughput automated small-angle X-ray
scattering data reduction and preliminary analysis.* S. S. Nielsen, K. Noergaard
Toft, D. Snakenborg, M. G. Jeppesen, J. K. Jacobsen, B. Vestergaard, J. P.
Kutteraand L. Arleth. Journal of Applied Crystallography (2009), 42, 959-964.

DOI: `10.1107/S0021889809023863 <https://doi.org/10.1107/S0021889809023863>`_


ATSAS
-----

If you use RAW to control any of the ATSAS programs (
`AMBIMETER <https://biosaxs-com.github.io/atsas/4.0.0/manuals/ambimeter.html>`_,
`DAMMIF <https://biosaxs-com.github.io/atsas/4.0.0/manuals/dammif.html>`_,
`DAMMIN <https://biosaxs-com.github.io/atsas/4.0.0/manuals/dammin.html>`_,
`DAMAVER <https://biosaxs-com.github.io/atsas/4.0.0/manuals/damaver.html>`_,
`DAMCLUST <https://www.embl-hamburg.de/biosaxs/manuals/damclust.html>`_,
`DATCLASS <https://biosaxs-com.github.io/atsas/4.0.0/manuals/datclass.html>`_,
`GNOM <https://biosaxs-com.github.io/atsas/4.0.0/manuals/gnom.html>`_,
`SASRES <https://biosaxs-com.github.io/atsas/4.0.0/manuals/sasres.html>`_,
`SUPCOMB <https://www.embl-hamburg.de/biosaxs/manuals/supcomb.html>`_,
`CIFSUP <https://biosaxs-com.github.io/atsas/4.0.0/manuals/cifsup.html>`_,
`CRYSOL <https://biosaxs-com.github.io/atsas/4.0.0/manuals/crysol.html>`_),
in addition to the RAW paper, please cite the appropriate paper given on their
`documentation pages <https://biosaxs-com.github.io/atsas/>`_.


BIFT
-----------

If you used the BIFT method to determine a P(r) function in RAW, in addition to
the RAW paper please cite the following paper:

*Bayesian estimation of hyperparameters for indirect Fourier transformation in
small-angle scattering.* Hansen, S. Journal of Applied Crystallography (2000),
33, 1415-1421.

DOI: `10.1107/S0021889800012930 <https://doi.org/10.1107/S0021889800012930>`_


Evolving Factor Analysis (EFA)
-------------------------------

If you used the EFA function in RAW to deconvolve overlapping chromatography data,
in addition to the RAW paper please cite the following paper:

*Domain Movements upon Activation of Phenylalanine Hydroxylase Characterized by
Crystallography and Chromatography-Coupled Small-Angle X-ray Scattering.* S. P.
Meisburger, A. B. Taylor, C. A. Khan, S. Zhang, P. F. Fitzpatrick, N. Ando.
Journal of the American Chemical Society (2016), 138(20), 6506-6516.

DOI: `10.1021/jacs.6b01563 <https://doi.org/10.1021/jacs.6b01563>`_


DENSS Tools
-------------------------------

Electron Density (DENSS)
^^^^^^^^^^^^^^^^^^^^^^^^^

If you used the electron density (DENSS) function in RAW to calculate electron density,
in addition to the RAW paper please cite the following paper:

*Ab initio electron density determination directly from solution scattering data.*
T. D. Grant. Nature Methods (2018), 15, 191–193.

DOI: `10.1038/nmeth.4581 <https://doi.org/10.1038/nmeth.4581>`_

Denss IFT (DIFT)
^^^^^^^^^^^^^^^^^^

If you used the DENSS IFT calculator (DIFT) in RAW, in addition to the RAW paper
please cite the following paper:

*Describing small-angle scattering profiles by a limited set of intensities.*
T. D. Grant. Journal of Applied Crystallography (2022), 55(5), 1116-1124.

DOI: `10.1107/S1600576722006598 <https://doi.org/10.1107/S1600576722006598>`_

PDB2SAS
^^^^^^^^^^^^

If you used the PDB2SAS theoretical profile aclculator in RAW, in addition to
the RAW paper please cite the following paper:

*Fitting high-resolution electron density maps from atomic models to solution
scattering data.* S. R. Chamberlain, S. Moore, and T. D. Grant. Biophysical
Journal (2023), 122(23), 4567-4581.

DOI: `10.1016/j.bpj.2023.10.034 <https://doi.org/10.1016/j.bpj.2023.10.034>`_



REGularized Alternating Least Squares (REGALS)
-----------------------------------------------

If you used the REGALS function in RAW to deconvolve SAXS data,
in addition to the RAW paper please cite the following paper:

*REGALS: a general method to deconvolve X-ray scattering data from evolving
mixtures* S. P. Meisburger, D. Xu, and N. Ando. IUCrJ (2021), 8(2), 225-237.

DOI: `10.1107/S2052252521000555 <https://doi.org/10.1107/S2052252521000555>`_

REGALS source code is available here: `https://github.com/ando-lab/regals <https://github.com/ando-lab/regals>`_


Molecular Weight
-------------------------------

Volume of Correlation
^^^^^^^^^^^^^^^^^^^^^^

If you used the volume of correlation method to determine molecular weight in RAW,
in addition to the RAW paper please cite the following paper:

*Accurate assessment of mass, models and resolution by small-angle scattering.* Rambo,
R.P. & Tainer, J.A. Nature (2013), 496, 477-481

DOI: `10.1038/nature12070 <https://doi.org/10.1038/nature12070>`_

Corrected Porod Volume
^^^^^^^^^^^^^^^^^^^^^^^

If you used the corrected Porod volume method to determine molecular weight in RAW,
in addition to the RAW paper please cite the following paper:

*SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute
solution from experimental SAXS data measured on a relative scale.* V. Piiadov,
E. Ares de Araujo, M. Oliveira Neto, A. F. Craievich, and I. Polikarpov.
Protein Science (2019), 28(2), 454-473.

DOI: `10.1002/pro.3528 <https://doi.org/10.1002/pro.3528>`_

Bayesian Inference
^^^^^^^^^^^^^^^^^^^^^

If you used the Bayesian inference method (datbayes) to determine molecular
weight in RAW, in addition to the RAW paper please cite the following paper:

*Consensus Bayesian assessment of protein molecular mass from solution X-ray
scattering data.* Hajizadeh, N. R., Franke, D., Jeffries, C. M. & Svergun, D. I.
Sci. Rep. (2018), 8, 7204.

DOI: `10.1038/s41598-018-25355-2 <https://doi.org/10.1038/s41598-018-25355-2>`_

Comparison to known structures
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

If you used the comparison to known structures (Shape&Size) method to determine
molecular weight in RAW, in addition to the RAW paper please cite the following
paper:

*Machine Learning Methods for X-Ray Scattering Data Analysis from
Biomacromolecular Solutions* Franke, D., Jeffries, C. M. & Svergun, D. I.
Biophys. J. (2018), 114, 2485–2492.

DOI: `10.1016/j.bpj.2018.04.018 <https://doi.org/10.1016/j.bpj.2018.04.018>`_


Baseline Correction
----------------------

If you used the integral baseline correction method in RAW, in addition to the RAW
paper please cite the following paper:


*US-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of
pure component patterns from poorly resolved SEC-SAXS data.* E. Brookes,
P. Vachette, M. Rocco, and J. Pérez. Journal of Applied Crystallography (2016),
49, 1827-1841.

DOI: `10.1107/S1600576716011201 <https://doi.org/10.1107/S1600576716011201>`_
