Saxier Forum

The online version of Coral uses the default weight of cross penalty. Apparently it is not enough for your samples.
For the time being could you please run local version of Coral in the expert mode and try to increase the cross penalty weight.

I've used the crysol binary from Atsas-3.0.1 release and obtained the attached fit file.
The obtained chi^2 value is 3.355. The chi^2 computed from the fit file taking lines 3 to end is also 3.355.
Can you reproduce this result?

Could you please attach the resulting fit file?

It does polynomial smoothing of the non-negative data. If the smoothed array still has significant systematic
deviations, 3% relative error is assigned.
In practice, the third column in the resulting *.fit file is the used error value.

Hi Thiago, so far there is no publication dedicated to FlexBin

Cryson automatically fits the background, so the deviation from the experimental data is simply a constant

The possible problem is that the zip file contains a folder with pdb files, whereas they should be in the root of the zip. If this condition is fulfilled and still there are complaints, then could you please send the zip for testing

1. Crysol not only evaluates the element, but rather an atomic group,
e.g. C, CH, CH2, CH3. For this the complete atomic name is needed.

2. Only the ions that are in close vicinity to the RNA should be kept

Hi Anthony, I've been able to run the following command on Win 10, Atsas 2.8.4 without any problems crysol K16Abilayer_no_metal_optimized_SPC_frame150_exported_watersdeleted_Cldeleted_unboundHdeleted.pdb -sm 2.0 -ns 201 Which platform/Atsas version do you use? Try maybe to shorten the pdb file name ...

Hi Anthony,
Could you please attach the PDB file causing the error?

Indeed it is currently not possible to provide the User-defined contrasts of the hydration shell(s) in Crysol 3.0.
It can be enabled in the future Atsas releases

It seems that the experimental data are in inverse angstroems,
but 1/nm is given as the input. Try to rerun with proper units.

Could it be that your construct contains multiple chains
and neither of the input PDB files is a multimer?

In such a case eom requires that a contacts file is provided

Given that the penalty is zero, the contacts restraints should be fulfilled.
Could you post the input files to check?

It might be that the dimer is not consistent with the SAXS data.

What is the resulting chi^2 and the contact penalty (in the header of the generated PDB file) ?