SAXS

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) ?

You could try the following conditions:

dist 5.0
1 41 41 2 262 262
dist 5.0
1 62 62 2 238 238

One can simply fix domains 1 and 4 in EOM, so that the desired interface is maintained

You could use Crysol to compute the fit from "6. Simulated protein and DNA complex" to "1. SAXS profile of protein and DNA complex" If the resulting fit is not good Sasref can be applied to arrange "4. Simulated DNA helix in pdb format" and "5. Crystal structure of the protein" to fit "1. SAXS profi...

Please note just in case that in the Coral contact conditions one should refer to the chain number, not domain number. Further, the current Coral version concatenates all the chains into one master chain and uses GLY as DR name identifier. The clarity of the output should be improved in the future r...

One can change "WAT" to "H2O" for example and then use "-eh" and "-dro=0" keywords in the command line