SAXS

prithaghosh wrote: ↑

2019.02.27 11:38

my models are that of RNA and not protein.

That doesn't matter - FFMAKER uses CRYSOL to calculate the intensities.

aga wrote: ↑

2018.12.31 07:06

the program just quits without warning or error message, or crashes.

We could not reproduce this. You should get an error message like "Domain 2: fixation is not compatible with initial configuration"; CORAL will exit with a non-zero exit code. Please make sure you use the latest ATSAS package.

Yes, sure, why not? You could have run FFMAKER/OLIGOMER on all ten of them to begin with.

... However, the experimental curve has a local minimum in I(q) at q=0, whereas my I(q) curve generated from CRYSOL has a maximum at q=0. (1) My first question is, why is this the case? Hard to tell. Collecting scattering data close to q=0 is challenging - that's where the primary beam hits the bea...

So, I used Crysol to simulate the scattering of the models generated by the EOM software and noticed a discrepancy between the values of Rg and Dmax obtained using the two softwares. What was the difference? 1%? 10%? What values from the CRYSOL log did you use as R g and D max ? (Should be "Rg from...

anlarsen wrote: ↑

2019.01.24 10:06

most SANS beamlines nowadays provide the resolution effect via an uncertainty of q, in the fourth column of data.

Could you please point us to some documentation on how the fourth column should be interpreted? So far we've seen SANS data in four-column format only from KWS1 (FRM2, Munich).

I am always getting the error that 'Domain 6 fixation is incompatible with the initial configuration' after grouping the domains. I am grouping (1,2), (4,5) and (3,6) domains. This means the domains 3 and 4 cannot be reasonably connected by a linker (given the distance between 5 and 6). There is no...

aga wrote: ↑

2018.12.31 07:06

I'm using it for the first time, so not sure where is the error in the con file...

Does CORAL online work for you?
*ATSAS online account required

akgupta wrote: ↑

2018.12.21 17:34

I just wanted to know what are the topics will be covered in this workshop? WIll you cover theory part as well?

Sure, a bit of theory, a bit of practice, a quite broad range of topics will be covered. Please check the AWSAXS2019 Program for details.

https://www.embl-hamburg.de/biosaxs/img/awsaxs2019.png ASEAN Workshop on Small Angle X-ray Scattering 19 - 26 February 2019 SLRI, Thailand The ASEAN Workshop on SAXS targets scientists, researchers, lecturers, postdocs and PhD students who are interested in determination of protein structure in sol...

2) Final Radius of gyration calculated from pdb file, after fitting to the experimental curve - is this "Theoretical Rg" or "Rg" in crysol_summary.txt Yes, this value is called: "Rg from the slope of net intensity" in the log file; in 'crysol_summary.txt' it is called "Theoretical Rg" if CRYSOL was...

I just started to used the new version of Primus (from 2.8.3 package)... If your OS is Windows or Linux - please note that the latest package is 2.8.4. (If you have a Mac please stick to 2.8.3 for now.) I was wondering if there was any help/manual with further details about the different results, s...

You should use I(q) vs. q background-subtracted experimental data files (*.dat) in ASCII format containing 3 columns: (1) momentum transfer q, (2) experimental intensity I(q) and (3) experimental errors.
Before interpreting the Rg histograms make sure the fit to your data is good.

How are the intensity profiles from given own pool of pdbs are created if the pool is not generated by RANCH? If you used your own pool of models then RANCh was not involved. The intensities are calculated by CRYSOL if you run GAJOE with the --pool option . Also in the log file, the pdb models are ...

I am using one program that can only process SAXS data containing 256 or less data points. ... ENSEMBLE contain three external programs and one of them is CRYSOL. I guess your question about rebinning data is already answered . But where does the 256 points limitation come from? CRYSOL can compute ...