Saxier Forum

benM wrote: ↑2023.09.22 15:23I cannot find the .dmg to install ATSAS on a mac OS Monterey. Would someone be kind enough to send me a link where I can find the proper .dmg ?

It's under Download ATSAS/3.2.1/MacOS/ATSAS-3.2.1-1.dmg

DigiCert changed the certificate validation procedure and it takes them ages to verify saxier.org. We all hope that it will be fixed soon!

I have been trying to understand how my protein is binding to DNA in my SAXs data and understand that NMATOR is best for this. Well, not really. NMATOR can bend your DNA or protein in various ways using normal mode analysis (NMA) to approximate the flexible motions of the molecule. I think it can t...

"Monodisperse" typically means that the scattering data are from a solution of particles of only one type, e.g. only protein dimers or only one kind of RNA. If you are referring to the program GNOM then "arbitrary monodisperse" means its default mode (or "system type" o...

Please add a space between '--prefix pool/' and 'assign.txt': ranch --repetitions 10 --prefix pool/ assign.txt sequence.fasta Without the space, ranch interprets your prefix as "pool/assign.txt" and the assignment file as "sequence.fasta", the third SEQUENCE FILE is missing. Make...

EMBL course on solution scattering from biological macromolecules 6 - 10 November 2023 ← virtual 27 November - 1 December ← EMBL Hamburg The Course is aimed at advanced PhD students, postdocs and junior researchers. The virtual module lectures will cover the basics of SAXS/SANS, instrumentation, da...

I guess you first need to run RANCH to create a pool of the models that you want to fit to your SANS data, then run CRYSO N on them, then run FFMAKER on the *.int files, then run GAJOE or NNLSJOE. The commands will be something like mkdir pool ranch sequence.seq assignment.txt --prefix=pool/model --...

Could you please clarify what you mean by "obviously wrong"? For all three data sets the residual difference plots look like noise around zero without systematic deviations and within three sigma. For c=0.27 mg/ml the X 2 =1.0 - this is by all standards a good fit . You can check the p-val...

I think you can fit your input data with OLIGOMER . GASBORMX saves the scattering computed from the monomer and oligomer as 'xxx-monomer.dat' and 'xxx-oligomer.dat' (where xxx is the name of your "project"). Try: ffmaker xxx-monomer.dat xxx-oligomer.dat --output=ff.dat oligomer --ff ff.dat...

To reduce termination effects – artificial oscillations in the p(r) function, which are caused by the absence of scattering data at higher angles – add a tail, something like

datft --tail=10000 --rmax=120 --nr=1201 --stop-at-zero data-calculated-from-model.abs --output pddf.dat

Unfortunately, there is no standard manual for DATFT but section 3.3 of the ATSAS 3.0 paper describes DATFT concisely and in detail. As with all ATSAS command line programs, you'll get a brief description of the available options by typing 'datft -h'. No idea what program was used for these figures,...

AUTORG and GNOM expect experimental data with some noise and uncertainties in the third column. Both programs will add some relative uncertainties if there were none in the input file, that's what the "ERREST" warning in GNOM is about. AUTORG may not fit the Guinier part of your simulated ...

Damsup was a convenience tool that was just running SUPCOMB.
In ATSAS 3.1 SUPCOMB was replaced by CIFSUP. Run it like this:

cifsup --method=nsd template-model.pdb my-model.pdb --output=my-model-rotated.pdb

SREFLEX works only with proteins. For DNA please use NMATOR.

0.7 Å is 2% of your theoretical R g . A Guinier R g estimate may come with a standard deviation, e.g. on this nice glucose isomerase data AUTORG estimates an R g of 32.3 Å with a standard deviation of 0.3 Å (just 1% - which is normal for low-noise data). But if we calculate the R g from the slope of...