Saxier Forum

DAMAVER got a major upgrade in the ATSAS 3.1 release: damsel, damsup, damaver, damfilt, damclust were integrated into DAMAVER; additional superposition methods were implemented; the list of the options is now different; the output is now in cif format (instead of pdb ) etc. Perhaps the Scatter and ...

What operating system (Windows, Ubuntu, macOS...) do you have?

On Ubuntu try typing 'primus' in the terminal.
On Windows go to Start > All apps > ATSAS > SAS Data Analysis
or open 'cmd' and type 'primusqt'.

Check out the YouTube video SAXS: what is a good fit? / How to run CRYSOL - it briefly explains what a good chi-squared value is (and what a correlation map test is).

Unfortunately it is not possible. But you may convert .cif to .pdb using cif2pdb : cif2pdb --help Usage: cif2pdb [OPTIONS] <FILE> Convert (a model from) mmCIF file format to PDB. Known Arguments: FILE mmCIF or PDB file Known Options: -o, --output=<FILE> Output filename (default: stdout) --model=<ID>...

BD wrote: ↑2022.01.17 13:28I do know what residue of protein A interacts with the disordered C-terminus. Can I impose this contact condition even though the C-terminus is not part of the crystal structure of protein B?

Yes, you can run CORAL on your PC and specify the contact in a contact conditions file.

It is unclear what OS you are on and what version of PyMOL you have. Please make sure that you have the latest ATSAS version and that you have followed the ATSAS installation guideline for your OS/package. Try to remove SASpy from PyMOL, remove ATSAS, reinstall ATSAS and reinstall SASpy.

Database of small-angle scattering data and models for biology and soft matter SAS_BSOFT online workshop, May 12-13, 2022 Despite the broad use of SAS in soft matter no public repository of data, parameters and models was available so far. The SASBDB framework offered a possibility to also cover th...

... Moreover, I always receive following message: “Warning: truncating input data to length: 2048” This means your experimental data contains more points than CORAL can handle and only the first 2048 points are taken for fitting. Does the molecular weight estimated from your SAXS data correspond to...

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Does the full path to your pdb or dat files contain Japanese characters? If yes - please try moving your files to a directory which has only Latin characters - does this help?

Please consider upgrading your Ubuntu. Standard support for Ubuntu 16.04 ended in April 2021.
The last ATSAS version available for Ubuntu 16.04 is 3.0.3.
ATSAS 3.1.0 prerelease is not available for Ubuntu 16.

When fitting the experimental input data, BUNCH uses the scattering intensity computed from the model + constant . This constant helps to adjust for imperfect background subtraction. If this constant becomes too negative, the overall predicted intensity becomes negative at some q values and this war...

Unfortunately, there is no official ATSAS release for Fedora. The CentOS 8 package would be the closest, we assume that you have tried that one. It looks like that the Qt platform plugin "xcb" for CentOS 8 is not compatible with Fedora 34. Please consider running ATSAS on one of the suppor...

Thank you for reporting this. Currently, OLIGOMER cannot handle more than 50 experimental data files or more than 50 form factors. Please organize your input data in groups of 50 files or less and run OLIGOMER on each group separately. The 'oligomer.log' will be appended, not overwritten. Apologies ...

How about running 'datcmp --format=CSV'?
To see all options please run 'datcmp --help'.

Running OLIGOMER on a single model doesn't make any sense, please run CRYSOL instead. But FFMAKER should actually work in your case without this awkward error. Are you sure that you have the latest ATSAS version installed? If you do - could you please share your 'model.pdb' with the ATSAS Team (or j...