SAXS

You may take any "template" curve, run pddffit, then remove the second and third column from the output file.

Sure, it is called pddffit. $ pddffit --help Usage: pddffit <PDDFFILE> <DATFILE> [OPTION] Fits a pair distance distribution function to experimental data. Known Options: -o, --output=FILE write the output to this file instead of stdout -v, --version print version information and exit -h, --help prin...

Due to multiple gentle requests, we have decided to reopen the Course registration. The new deadline is August 31 2019.

Thank you for sending the files. The sequence file name contains spaces, apparently, this is not allowed. Please replace spaces with e.g. underscores and EOM will start.

In order to reproduce the problem we'd need all the files you have submitted. Could you please send us these files via email or post them here?

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Could you please change the extension of your sequence .fasta file to ".seq"?

DAMMIN online runs only once, DAMAVER does not run here. If you wish to re-run DAMMIN online please go to My Projects and click re-run with new id.

BioSAXS practical course 2019 CEITEC practical course, 10 - 11 September 2019, Brno, Czech Republic https://www.embl-hamburg.de/biosaxs/img/ceitec-course-brno.png A short practical course on basics of biological SAXS in Brno, Central European Institute of Technology (CEITEC) introducing the practic...

It looks like you are using an outdated Windows-only "QuickWin" version of DAMMIN. Please use the command-line version or use DAMMIN online.

I'm fitting some data and I was wondering how do you calculate the scaling factor present in the formula for chi^2 The scaling factor minimizes chi-squared (least squares method). and also, I would like to understand the k-1 factor...IN your paper there is not any explanation about that factor... N...

The theoretically generated scattering curves have a four to five fold difference in intensity than the experimental curves. Just treat the intensity of the theoretical curves as some arbitrary units and scale (multiply) them to match your experimental data. Please note that you may fit the compute...

Am I missing a setting to preserve residue order in the output PDBs? Hi Jesse, unfortunately that's how RANCH works - it calls everything chain A and the order of the residues is a complete chaos. We've opened a bug report for this issue. Perhaps there is a script that can properly rename the chain...

Loki03 wrote: ↑

2019.04.25 20:04

... it still asks for a sequence and then doesnt match it to the pdb that I glycosylated with the GLYCOSYLATION program.

So EOM runs fine with your domain(s) an the sequence before you run GLYCOSYLATION but after you run GLYCOSYLATION it says the sequence doesn't match?

prithaghosh wrote: ↑

2019.04.25 17:20

How can I output the theoretical I vs q curve for a model that is calculated by CRYSOL?

$ crysol model.pdb

The output file model00.int will contain the calculated scattering intensity.

MASSHA is available only on Windows. Please use the PyMOL plugin SASpy instead.
(The SASpy plugin from ATSAS 2.8.4 is for PyMOL version 2.2 or earlier.)