Search found 13 matches

by sjc
2017.08.17 17:44
Forum: Ab initio shape determination
Topic: DAMMIF in 2.8.2 generates very different models than 2.8.0
Replies: 0
Views: 10561

DAMMIF in 2.8.2 generates very different models than 2.8.0

Hi Saxier, Running DAMMIF from the newest ATSAS on the same profile as previous modelling runs, I get a model with much less contiguity and cavities in the centre of the particle. GASBOR has remained consistent with this profile and generates a compact particle. Are there changes in the most recent ...
by sjc
2017.08.14 16:12
Forum: Ab initio shape determination
Topic: DAMMIF defaults to prolate aniso, even when entering unk
Replies: 4
Views: 6374

Re: DAMMIF defaults to prolate aniso, even when entering unk

So if I understand correctly, DAMMIF now automatically assumes a shape class from the scattering profile and then uses this to constrain the refinement? In my case the shape class is reported as flat, which seems like the opposite of oblate, no? Log included below, only change is I've obscured the p...
by sjc
2017.08.08 22:24
Forum: Ab initio shape determination
Topic: DAMMIF defaults to prolate aniso, even when entering unk
Replies: 4
Views: 6374

DAMMIF defaults to prolate aniso, even when entering unk

Hi Saxier, I've noticed that when I run DAMMIF either interactively or from a script, that the particle anisometry defaults to prolate, even when I specify it to be unknown. When I don't indicate a value for anisometry, or when I enter Unknown, the log file indicates prolate anisometry. Is there a w...
by sjc
2017.08.01 19:23
Forum: SAS Experiment Design
Topic: I(0) of Kratky camera-smeared data
Replies: 0
Views: 10911

I(0) of Kratky camera-smeared data

Hi saxier forum users, I have a question that comes from the use of an Anton Paar SAXS instrument. In a slit-smeared experiment, is the I(0) of the smeared data still proportional to the scattering particles in the same way that it is for non-smeared data? I'm thinking specifically of how the I(0) i...
by sjc
2017.06.20 20:23
Forum: Mixtures and flexible systems
Topic: Using Oligomer for heterodimeric mixture
Replies: 1
Views: 1262

Re: Using Oligomer for heterodimeric mixture

I'm going to add a follow-up question, as I've been looking at how to build this model. As I understand, the example provided in ATSAS documentation number fractions means defines AB A B as 0.0, 1.0, -1.0, which constrains A and B to equal molar amounts in the refined proportions. I hope to leave A ...
by sjc
2017.06.09 17:59
Forum: Mixtures and flexible systems
Topic: Using Oligomer for heterodimeric mixture
Replies: 1
Views: 1262

Using Oligomer for heterodimeric mixture

Hi Saxier users, I'm probing a system in weak binding equilibrium with two different proteins. That means that in my capillary, I have Protein A, Protein B, and the A-B complex. I'm looking into using OLIGOMER to deconvolute the contributions of all three components by altering the molar ratios and ...
by sjc
2017.06.01 17:26
Forum: ATSAS package in general
Topic: Export Plots to Vector Format
Replies: 2
Views: 5790

Re: Export Plots to Vector Format

Thanks! Yes, since I posted I eventually settled on using gnuplot to make svg files, so I guess I was on the right track! Thanks for the reply!
by sjc
2017.05.23 17:14
Forum: ATSAS package in general
Topic: Export Plots to Vector Format
Replies: 2
Views: 5790

Export Plots to Vector Format

Hi saxier users, I have some data I'm preparing for publication, and one thing that would really help would be an easy way to export data to a vector format (svg, pdf, etc). As far as I can tell, PRIMUS and SASPLOT currently export just to png format. Is there a way to get a vector format export of ...
by sjc
2017.01.30 20:06
Forum: Rigid body modelling
Topic: Slit smearing in SASREF and BUNCH
Replies: 4
Views: 8277

Re: Slit smearing in SASREF and BUNCH

I know I'm about 7 years late to this thread, but I can't find any documentation about how BUNCH and SASREF handle the Kratky data. Can anyone point me in the right direction?
by sjc
2013.09.18 15:08
Forum: Rigid body modelling
Topic: BUNCH "Maximum radius" in prompt
Replies: 2
Views: 3420

Re: BUNCH "Maximum radius" in prompt

Awesome - thanks for the info!
by sjc
2013.06.11 01:14
Forum: Rigid body modelling
Topic: BUNCH "Maximum radius" in prompt
Replies: 2
Views: 3420

BUNCH "Maximum radius" in prompt

Hi - hopefully a quick question: In the BUNCH prompt, after loading the pre_bunch file, the prompt (and log file) report a "maximum radius". What does this value represent? Is it just half of the Dmax of the input model? Is this value used in the modelling process, or just a description of the input...
by sjc
2011.07.23 21:20
Forum: Rigid body modelling
Topic: BUNCH/SASREF/EOM Input files and alm's from domains
Replies: 0
Views: 3890

BUNCH/SASREF/EOM Input files and alm's from domains

Hi everyone, I guess this is more of an observation than a question as I think I've rooted out the problem, but thought I'd put it up here in case anyone else runs into similar issues modelling in the future. I had collected some "quick-and-dirty" data for a two-domain protein and modelled in two ri...
by sjc
2011.06.09 15:06
Forum: Rigid body modelling
Topic: Bunch Iterations and successes - Windows v8.0
Replies: 1
Views: 2272

Bunch Iterations and successes - Windows v8.0

Hi Everyone, I've been playing around with SAXS processing for a while now, and trying to debug some simulation runs where I'm modelling a 2-domain protein with flexible linker in BUNCH. I'm using ATSAS 2.4 for Windows, with BUNCH 8.0. Going through all the parameters, I noticed that while the bunch...