Saxier Forum

It looks like you don't have administrative rights to install programs to C:/atsas/ . If you are installing the latest version 3.0.1 it should suggest to install ATSAS to C:\Program Files (x86) . If that doesn't work, please try installing to your 'My Documents' folder, something like C:\Users\youru...

filport wrote: ↑

2020.05.19 14:54

"libgcc_s_sjlj-1.dll libgfortran-3.dll libsaxsdocument.dll" missing.

What command/program are you running before you see this message?

GNOM's number of points in real space cannot be higher than the number of input points in reciprocal space. And it cannot be more than 256. When you use GNOM from PRIMUSqt, the number of points might be automatically decreased when you decrease the input data range. Please note, the GNOM manual is a...

In addition, I am also looking for tips in manually calculating the Rg of samples, in excel, from raw .dat files. Any tips or best practices for this are appreciated, but not necessary. Excel might be a bit challenging. Try ATSAS AUTORG for an automatic Guinier approximation or DATRG for calculatin...

Thank you for reporting this. In the meantime here is the datmw --help output: Usage: datmw [OPTIONS] [FILE(S)] Molecular weight (MW) by multiple methods: --method=Porod MW from Porod Volume ( Petoukhov et al., 2012 ) Output: smax (A^-1), Volume (A^3), MW (Da), file name --method=Qp MW from Porod In...

https://www.embl-hamburg.de/biosaxs/courses/embl2020/img/poster-small.png Solution Scattering from Biological Macromolecules EMBL Online Lecture Course, May 5 - June 2, 2020 Tuesdays and Thursdays 9:20-10:30, CEST This online course aims at young biochemists/biophysicists and researchers active in ...

Indeed the manual has to be updated. Please run pre_bunch it like this: $pre_bunch sequence.seq domain1.pdb domain2.pdb --output my_pre_bunch.pdb For details see: $pre_bunch --help Usage: pre_bunch [OPTIONS] <SEQFILE> <FILE(S)> Generates an initial approximation for further use in BUNCH Known Argume...

han yin wrote: ↑

2020.03.17 13:48

...i could not open the supcomb command function: the command prompt window opens then instantly closes.

How to use the Windows command line
ATSAS: how to update/modify your PATH settings

Please install the SASpy plugin. Open your ab initio model and the crystal structure in PyMOL. Open SASpy, switch to the 'supalm' tab. Under 'Model selection' choose the two models and click 'Execute'. This will work well for globular models like lysozyme. If you have very elongated models it is bet...

oavina24 wrote: ↑

2020.02.21 09:26

What i meant to say is that if its necessary to increase the whole range of data when calculating the pair distance distribution.

Could you please rephrase your question?

Which input data file ? target.dat - it should contain the experimental SAXS data, three columns: q , I(q) , sigma(q) . ( q and s both mean the same). If your SAXS data file does not have the third sigma column then CRYSOL will invent the experimental errors and compute the chi-squared using these.

The experimental errors sigma(s) are taken from the input data file, third column.

The option to provide a single file listing the input models was removed a while ago. Please run DAMSEL like this instead:

damsel model-2-1.pdb model-1-1.pdb model-3-1.pdb model-4-1.pdb model-6-1.pdb model-5-1.pdb model-7-1.pdb model-8-1.pdb model-9-1.pdb

If your experimental SAXS data at q > 8/R_g is just noise around zero (check by plotting your data on an absolute scale) there is not much point in using GASBOR. Just use DAMMIF.

Download ATSAS 3.0.1 (academic users only) New platform: Debian 10. Framework changes: updated to Qt-5.12.6 and QtIFW-3.2.0: fixes the issue of numpad not working in primus/qt on Linux; fixes black text on black widget installer on MacOS with dark mode; fixes issues with the ATSAS environment varia...