SLIDE 1 From data to publication
Walk through ATSAS programs and data deposition
Al Kikhney EMBL Hamburg
Solution Scattering from Biological Macromolecules July 7, 2020
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- Over 90 programs
- Operating systems:
- Windows 8 and 10,
- macOS 10.12 Sierra, 10.13 High Sierra and 10.14 Mojave,
- Red Hat/CentOS 7 and 8,
- Ubuntu 16 and 18,
- Debian 9 and 10.
- Free for academic users:
https://www.embl-hamburg.de/biosaxs/download.html
ATSAS software package 3.0
- K. Manalastas-Cantos, P.V. Konarev, N.R. Hajizadeh, A.G. Kikhney, M.V. Petoukhov, D.S. Molodenskiy,
- A. Panjkovich, H.D.T. Mertens, A. Gruzinov, C. Borges, C.M. Jeffries, D.I. Svergun and D. Franke (2020)
ATSAS 3.0: Expanded functionality and new tools for small-angle scattering data analysis
- J. Appl. Cryst., submitted
SLIDE 3 https://www.embl-hamburg.de/biosaxs/software.html
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Primary data analysis Monodisperse systems Polydisperse systems
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Primary data analysis
data PRIMUS 2D image IM2DAT
SLIDE 6 Primary data analysis
data PRIMUS GNOM (PDDF) Ab initio modelling DAMAVER/DAMCLUST AMBIMETER
Most representative model(s)
- potentially unique
- might be ambiguous
SLIDE 7 Data from www.sasbdb.org/data/SASDFP8/
SLIDE 8 Data from www.sasbdb.org/data/SASDFP8/
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SLIDE 14 Command line tool: DATMW
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SLIDE 16 Command line tool: GNOM
SLIDE 17 https://www.embl-hamburg.de/biosaxs/dattools.html
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Ab initio modelling
Program When to use DAMMIF Always! (well, almost) DAMMIN If DAMMIF doesn’t fit; exotic symmetries GASBOR Proteins smaller than 660 kDa + good data at s > 8/Rg MONSA Complexes (e.g. protein:RNA) with multiple data sets, typically with SANS data www.embl-hamburg.de/biosaxs/atsas-online/
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Monodisperse systems
data model
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Monodisperse systems
data CRYSOL fit
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Monodisperse systems
SANS data CRYSON fit
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Monodisperse systems
data CRYSOL bad fit?
SLIDE 23 Monodisperse systems
data SREFLEX fit refined model
Flexible refinement using normal mode analysis
SLIDE 24 Monodisperse systems
data SREFLEX fits refined models
- Proteins only, full-length
- Works best on smaller proteins
- Symmetry is not supported
SLIDE 25 Monodisperse systems
data NMATOR fits refined models
Flexible refinement using NMA in dihedral/torsion angle space
SLIDE 26 Monodisperse systems
data SASREF fit complete model
Rigid body modelling of multisubunit complexes
SLIDE 27 Monodisperse systems
data SASREF fit complete model
- Complementary data from other methods
- Supports GLYCOSYLATION
- Contrast variation (SANS)
- Equilibrium mixtures
SLIDE 28 Monodisperse systems
data CORAL fit complete model
Modelling multidomain protein complexes against multiple data sets ? Missing linkers
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Monodisperse systems
CRYSOL/CRYSON SREFLEX/NMATOR SASREF CORAL www.embl-hamburg.de/biosaxs/atsas-online/
SLIDE 30 Polydisperse systems
SLIDE 31 Data from www.sasbdb.org/data/SASDFN8/
SLIDE 32 Data from www.sasbdb.org/data/SASDFN8/
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Polydisperse systems
data models
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Polydisperse systems
data OLIGOMER fit + volume fractions
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? ?
Polydisperse systems
data OLIGOMER fit?
SLIDE 37 Polydisperse systems
data SASREFMX fit complete model(s)
Rigid body modelling of equilibrium mixtures
SLIDE 38 Polydisperse systems
data.out GASBORMX fir oligomer model
ab initio reconstruction of protein oligomer:monomer mixtures
SLIDE 39 Polydisperse systems
data Ensemble Optimization Method fit + Rg histogram
EOM
protein sequence
+
RANCH & GAJOE
SLIDE 40 Polydisperse systems
RANCH
EOM
protein sequence
+
Generate a pool of RANdom CHain models
SLIDE 41 Polydisperse systems
RANCH
EOM
protein sequence
+
Generate a pool of RANdom CHain models
GAJOE fit + Rg histogram
EOM
Genetic Algorithm Judging Optimisation of Ensembles
data
SLIDE 42 Polydisperse systems
NMATOR GAJOE fit + Rg histogram
EOM
Genetic Algorithm Judging Optimisation of Ensembles
data
Custom pool
SLIDE 43 EOM
Polydisperse systems
OLIGOMER SASREFMX GASBORMX EOM www.embl-hamburg.de/biosaxs/atsas-online/
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SASpy – PyMOL plugin
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SLIDE 47 https://www.embl-hamburg.de/biosaxs/manuals/
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Can’t find a manual?
C:\data\SAXS> datop --help
SLIDE 49 Can’t find a manual?
C:\data\SAXS> Usage: datop [OPTIONS] <OPERATOR> <FILE1> <FILE2|X> Apply a mathematical operator to a pair of data files Known Arguments: OPERATOR Mathematical operator, one of ADD, SUB, MUL, DIV or NORM FILE1 First operand: data file FILE2|X Second operand: data file or numeric constant Known Options:
- o, --output=<FILE> File to save the result data (default: stdout)
- h, --help Print usage information and exit
- v, --version Print version information and exit
datop --help
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Data deposition
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Sharing unpublished data
SLIDE 57 https://www.sasbdb.org/draft-preview/359/h7w3ks5vvs/
SLIDE 58 https://www.sasbdb.org/data/SASDDN2/z6c25yspdo/
Unreleased
SASDDN2
SLIDE 59 https://www.sasbdb.org/data/SASDDN2/
Unreleased
SASDDN2
SLIDE 60 Thank you!
www.saxier.org/forum www.sasbdb.org biosaxs.com
