From data to publication Walk through ATSAS programs and data - PowerPoint PPT Presentation

From data to publication Walk through ATSAS programs and data deposition Al Kikhney EMBL Hamburg Solution Scattering from Biological Macromolecules July 7, 2020

ATSAS software package 3.0 • 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 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

https://www.embl-hamburg.de/biosaxs/software.html

Primary data analysis Monodisperse systems Polydisperse systems

Primary data analysis data IM2DAT 2D image PRIMUS

Primary data analysis data PRIMUS • potentially unique GNOM (PDDF) AMBIMETER • might be ambiguous Ab initio modelling DAMAVER/DAMCLUST Most representative model(s)

Data from www.sasbdb.org/data/SASDFP8/

Data from www.sasbdb.org/data/SASDFP8/

Command line tool: DATMW

Command line tool: GNOM

https://www.embl-hamburg.de/biosaxs/dattools.html

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/R g MONSA Complexes (e.g. protein:RNA) with multiple data sets, typically with SANS data www.embl-hamburg.de/biosaxs/atsas-online/

Monodisperse systems data model

Monodisperse systems data CRYSOL fit

Monodisperse systems SANS data CRYSO N fit

Monodisperse systems data CRYSOL bad fit?

Monodisperse systems data SREFLEX Flexible refinement using normal mode analysis fit refined model

Monodisperse systems data • Proteins only, full-length SREFLEX • Works best on smaller proteins • Symmetry is not supported fits refined models

Monodisperse systems data NMATOR Flexible refinement using NMA in dihedral/torsion angle space fits refined models

Monodisperse systems data SASREF Rigid body modelling of multisubunit complexes fit complete model

Monodisperse systems data • Complementary data from other methods • Supports GLYCOSYLATION SASREF • Contrast variation (SANS) • Equilibrium mixtures fit complete model

Monodisperse systems data CORAL ? Missing linkers Modelling multidomain protein complexes against multiple data sets fit complete model

Monodisperse systems CRYSOL/CRYSON SREFLEX/NMATOR SASREF CORAL www.embl-hamburg.de/biosaxs/atsas-online/

Polydisperse systems • SEC-SAXS

Data from www.sasbdb.org/data/SASDFN8/

Data from www.sasbdb.org/data/SASDFN8/

Polydisperse systems data models

Polydisperse systems data OLIGOMER fit + volume fractions

Polydisperse systems data OLIGOMER ? ? fit?

Polydisperse systems data SASREF MX Rigid body modelling of equilibrium mixtures fit complete model(s)

Polydisperse systems data.out GASBOR MX ab initio reconstruction of protein oligomer:monomer mixtures fir oligomer model

Polydisperse systems data protein Ensemble Optimization Method + EOM sequence RANCH & GAJOE fit + R g histogram

Polydisperse systems protein RANCH + EOM sequence Generate a pool of RANdom CHain models

Polydisperse systems protein RANCH + EOM sequence Generate a pool of RANdom CHain models data GAJOE fit + R g histogram EOM Genetic Algorithm Judging Optimisation of Ensembles

Polydisperse systems NMATOR Custom pool data GAJOE fit + R g histogram EOM Genetic Algorithm Judging Optimisation of Ensembles

Polydisperse systems OLIGOMER SASREFMX GASBORMX EOM EOM www.embl-hamburg.de/biosaxs/atsas-online/

SASpy – PyMOL plugin

https://www.embl-hamburg.de/biosaxs/manuals/

Can’t find a manual? C:\data\SAXS> datop --help

Can’t find a manual? C:\data\SAXS> datop --help 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

Data deposition

1/cm

Sharing unpublished data

https://www.sasbdb.org/draft-preview/359/h7w3ks5vvs/

https://www.sasbdb.org/data/SASDDN2/z6c25yspdo/ Unreleased SASDDN2

https://www.sasbdb.org/data/SASDDN2/ Unreleased SASDDN2

Thank you! biosaxs.com www.sasbdb.org www.saxier.org/forum