Search found 16 matches

by 123
2017.08.11 21:26
Forum: SAS Hardware/Instrumentation
Topic: X33 beam geometry
Replies: 1
Views: 18980

X33 beam geometry

Hi,

Could you please tell me what was the beam geometry at the X33 beamline? I need the information to provide in the SAXS table for a paper.

Thank you
by 123
2015.05.22 16:42
Forum: Primary data processing
Topic: Two concentrations, two curves
Replies: 6
Views: 5675

Re: Two concentrations, two curves

The two curves are attached. The change in Rg is small so I'm not sure about inter-particle interactions.
Thanks!
by 123
2015.05.21 23:46
Forum: Primary data processing
Topic: Two concentrations, two curves
Replies: 6
Views: 5675

Re: Two concentrations, two curves

Thanks for your response Alex. The two curves will never overlay no matter how they are scaled. I don't think it makes sense to merge them without having them on the same scale. Any suggestions?
by 123
2015.05.20 16:16
Forum: Primary data processing
Topic: Two concentrations, two curves
Replies: 6
Views: 5675

Re: Two concentrations, two curves

any comments on this?
by 123
2015.05.16 21:18
Forum: Primary data processing
Topic: Two concentrations, two curves
Replies: 6
Views: 5675

Two concentrations, two curves

Hi all,

I've measured SAXS on a ~23 kDa protein at two concentrations (2.5 mg/ml and 5 mg/ml). The scaled curves (ATSAS 2.6) are attached.
Are these differences due to buffer subtraction? Should I merge or just use one of the curves?

Thank you for your suggestions.
by 123
2013.05.09 15:37
Forum: Primary data processing
Topic: odd datgnom Dmax selection
Replies: 2
Views: 4103

Re: odd datgnom Dmax selection

Interesting point. I also get a Dmax of 3.5*Rg from DATGNOM. Any comments from the developers?
by 123
2013.05.07 12:03
Forum: Ab initio shape determination
Topic: quick monsa question
Replies: 7
Views: 9644

Re: quick monsa question

Once, I heard rumours that the molecular masses are a good estimate, because only the ratio matters and to a first approximation is similar enough, i.e. V1/V2 \approx M1/M2. For protein-protein complexes yes. But RNA has a different density, I think slightly higher than protein. Maybe it doesn't ma...
by 123
2013.05.03 21:33
Forum: Ab initio shape determination
Topic: quick monsa question
Replies: 7
Views: 9644

Re: quick monsa question

56 25 80 0.0 ! Desired Volumes I have a question about the Desired volumes. For a complex of protein and nucleic acid how does one estimate these? Based on molecular mass? or is it better to use DAMMIF volumes? How important is it to enter a correct value for this parameter? Thanks!
by 123
2013.04.29 15:16
Forum: Primary data processing
Topic: primusqt design
Replies: 6
Views: 6005

Re: primusqt design

This is because the data was cropped at the beginning, whereas the theoretical curve is calculated from
S=0
Thanks Alex, but I think I get this even with data which is not cropped .I'll check again.
by 123
2013.04.29 14:49
Forum: Primary data processing
Topic: primusqt design
Replies: 6
Views: 6005

Re: primusqt design

On a related note: What is this step line in the beginning of the experimental data shown above? I also noticed this when I was looking at CRYSOL fits in sasplot. Is there an easy way to get rid of it?
by 123
2013.04.20 14:54
Forum: Mixtures and flexible systems
Topic: EOM problem on Windows 7
Replies: 1
Views: 2979

EOM problem on Windows 7

Dear all, I tried to run EOM (in ATSAS 2.51 package) on my laptop and it took almost 3 hours to create the 10,000 models. Then it said: "... finished the GENETIC ALGORITHM! Remaking selected structures..." and then it crashed!!! Does anyone know what the problem is? Also the pdb files are not saved ...
by 123
2013.04.19 20:20
Forum: Mixtures and flexible systems
Topic: eom for rna?
Replies: 10
Views: 8635

Re: MC-Fold|MC-Sym

Use the MC-Fold|MC-Sym pipeline to generate a large number of RNA structures. Then check with CRYSOL if one of them fits the SAXS data. If not a single structure fits and you think that your RNA is flexible in solution - it is possible to use EOM on these structures. @Al I have used this strategy b...
by 123
2013.04.19 20:09
Forum: Model evaluation and manipulation
Topic: Trouble understanding DAMAVER result
Replies: 3
Views: 8467

Re: Trouble understanding DAMAVER result

@Al could you please explain why "Use SUPCOMB on the "Reference" model, not on the damfilt.pdb"? Isn't the damfilt.pdb the more corect representation?
by 123
2013.04.11 23:27
Forum: Ab initio shape determination
Topic: Question about DAMMIF online version
Replies: 7
Views: 7594

Re: Question about DAMMIF online version

Any answers to renje464 questions?
It would be great to get some information about the different outputs of online DAMMIF. I couldn't find this described anywhere.

Thanks!
by 123
2013.04.09 20:00
Forum: Primary data processing
Topic: s = 8/Rg rule with Gnom
Replies: 3
Views: 6500

Re: s = 8/Rg rule with Gnom

Hi,

Could you please give a reference to this 8/Rg rule. What I heard was 7/Rg, is this something empirical?
Also if I want to just show few P(r) curves for comparison which q(or s)max should I use? Is it ok to show the whole range?

Thanks in advance!