SAXS

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

Please note that the formfactors are still computed from Gaussian spheres, not solid spheres

Fraser et al. (1978) lists observed volumes for just four atoms.
The present version of Crysol supports 108 atom and atomic groups (e.g. CH)
whose Wan-der-Waals volumes seem to work well.

In Cryson the form factors for individual atoms are constants equal to the corresponding scattering lengths
but for the atomic groups (like CH) the formfactors are computed using the Debye formula and therefore depend on s.

Incoherent scattering is not taken into account in prediction mode.

Dry volume is simply computed from the molecular weight as V=1.21*MW where MW is in Dalton and V is in A^3. Displaced volume is the sum of the Van-der-Waals volumes of individual atomic groups, (i.e. it serves as V0 in formula). Excluded volume is the adjusted value (V in the formula, in prediction ...

Hi,

Internally Coral puts all the input proteins into one "superchain",
therefore the reported numbering is different from the dist.cnd.
Have you checked that the conbdition is fulfilled in the resulting model?

The smearing is done according to the equation (9.26) from Feigin&Svergun book, page 295 with W(t)=2*Smax (i.e. constant) corresponding to an infinite slit.

If PDB file contains standard atoms, one can use Crysol in the same way as for biological molecules