Search found 103 matches

by Hayds
2010.11.16 15:19
Forum: Primary data processing
Topic: Interpretation of differences between scattering curves
Replies: 5
Views: 4187

Hi Chiara, it looks as if the model systematically deviates from the SAXS data in all three cases, although the overall dimension is about right. What region did you use for scaling the overlay (assuming they were scaled)? There is a hint that the green curve describes a larger particle than the oth...
by Hayds
2010.11.16 10:13
Forum: Primary data processing
Topic: Interpretation of differences between scattering curves
Replies: 5
Views: 4187

Hi Chiara, when you overlay the curves do they differ at any point? I am tempted to say that no reliable conformation change has been detected, as I see no obvious deviations in the curves. It is hard to detect small changes upon ligand binding, it is much easier when a large change occurs that impa...
by Hayds
2010.10.23 23:58
Forum: Announcements
Topic: Course on solution scattering from biological macromolecules
Replies: 6
Views: 23269

:(

How come I don't get officially listed as a tutor :cry:

Don't you like me any more Al?

;)
by Hayds
2010.10.22 15:32
Forum: Ab initio shape determination
Topic: Supported symmetries in Gasbor
Replies: 5
Views: 3855

Thanks Tanya,

We should include a description to go with the symmetry options in each package manual I think.

Thanks for pointing that out, it helps a lot with the program development.

Best,

Haydyn
by Hayds
2010.10.22 09:31
Forum: Ab initio shape determination
Topic: Supported symmetries in Gasbor
Replies: 5
Views: 3855

Hi Tanya,

you are correct. The crystallographic symmetry P6_5 is not supported.

Sorry,

Haydyn
by Hayds
2010.10.20 18:08
Forum: Ab initio shape determination
Topic: Supported symmetries in Gasbor
Replies: 5
Views: 3855

GASBOR symmetry

Hi Tanya,

I think everything supported is listed here:

http://www.embl-hamburg.de/biosaxs/manual_gasbor.html

Hope it helps,

Haydyn
by Hayds
2010.10.20 13:36
Forum: Primary data processing
Topic: Picture export in Primus
Replies: 7
Views: 6530

Hi Spark, most people in the group export the data to sigmaplot and manipulate it to re-create the Guinier plot inside that program. This gives nice pictures. You can also try the open source project saxsview: http://saxsview.sourceforge.net/ You will need to convert the data into a Guinier plot (Ln...
by Hayds
2010.10.14 23:19
Forum: Model evaluation and manipulation
Topic: Damsel.log and damsup.log
Replies: 1
Views: 3093

Hi Helle, the average NSD helps to define clear outliers. Models whose NSD exceeds 2 standard deviations from the mean are considered outliers and will be excluded from the selection of the most representative model. damsup.log lists the NSD between the representative model and each listed model. da...
by Hayds
2010.10.14 23:00
Forum: Mixtures and flexible systems
Topic: two protein complex - or not?
Replies: 2
Views: 3876

Dear Jak, Did you run a concentration series on your "complex" sample (and maybe various molar ratios)? You should be able to follow changes in Rg, Dmax and volume. This should help you to determine if you form the complex or not. You also indicate that you have data for the individual components so...
by Hayds
2010.10.14 22:39
Forum: Mixtures and flexible systems
Topic: EOM
Replies: 2
Views: 3208

Hi Liz, That is an interesting point. Can you check that upon visual inspection of the curves for the best and worst CRYSOL model fits that the fits are OK? It happens often that people rely only upon CHI without looking for systematic deviations in the fits. Also, did you use constant subtraction i...
by Hayds
2010.10.08 19:33
Forum: Mixtures and flexible systems
Topic: Check fit with alternate EOM ensemble
Replies: 6
Views: 5217

Hi jonathan, For OLIGOMER I would extract the 2nd column (Theoretical scattering intensity) from each CRYSOL .int file and paste them into one file (also including the 1st column from one of the CRYSOL .int files, this will be column 1, the s-values, for the combined file). This should give you an i...
by Hayds
2010.10.08 14:01
Forum: Mixtures and flexible systems
Topic: Check fit with alternate EOM ensemble
Replies: 6
Views: 5217

Hi jonathan, So, running OLIGOMER on the EOM selected ensemble should, in principle replicate the GAJOE fit, and you can fit multiple SAXS data sets to the ensemble this way. This should also weight the samples by volume fraction which should account for any "replicates" that were used in EOM. To di...
by Hayds
2010.10.08 10:20
Forum: Mixtures and flexible systems
Topic: Check fit with alternate EOM ensemble
Replies: 6
Views: 5217

Hi Jonathan, You should be able to run CRYSOL acrosss the ensemble and then create an average scattering curve from the calculated intensity files. You should then be able to fit this averaged curve to the data. Note that if you ran GAJOE in default mode then you allow repetitions (ie. the same stru...
by Hayds
2010.10.04 10:06
Forum: Mixtures and flexible systems
Topic: Check fit with alternate EOM ensemble
Replies: 6
Views: 5217

Hi jpruneda. This is quite straight forward, you need to rename the size list file in the top level of your EOM directory and rerun GAJOE with the new data file. eg. If your new data file name is DATA.dat (1) rename Size_listDATA.txt (eg. from the previous run it was named something like Size_listOL...
by Hayds
2010.09.27 22:34
Forum: Literature
Topic: SAS Studies of Biological Macromolecules in Solution
Replies: 1
Views: 12628

Structural characterization of proteins and complexes

Hi all, shameless plug for the new review from the Hamburg SAXS group: Mertens H. D. T. & Svergun D.I. Structural characterization of proteins and complexes using small-angle X-ray solution scattering J Struct Biol. 2010 Oct;172(1):128-41. Small-angle scattering of X-rays (SAXS) is an established me...