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I think the solvent masking is not estimated correctly if only a PDB file is provided (i.e. no experimental data) to SFcalculator.
This is observable in the real space electron density (e.g if loaded in Coot).
I believe the issue is that the scales are not initialized to good enough values when data is not provided.
But at the very least kmask should be resolution dependent with some average values. The following seems to work well and gives good real space density for a few test cases:
I use the kmask expression: kmask = ksol * exp( -Bsol * s**2 /4) with ksol = 0.85 (midway between 0.75-0.95)
and Bsol = 250 (midway between 150-350) from Glykos & Kokkinidis, Acta Crystallogr D Biol Crystallogr. 2000 Aug;56(Pt 8):1070-2
These are probably not the most representative values, but they seem to do the trick. Thoughts?
The text was updated successfully, but these errors were encountered:
Sorry for the late reply. Before we were thinking the solvent mask is used as a modeling for better fitting the experimental observables, so it was not clear about how to apply a solvent mask without experiments.
But the values you provided all make sense. Also I feel this could be used to implement a new method to generate synthetic crystallography observables when only PDB is provided. I am working on the implementation and will create a PR in the torch version. Thanks for the suggestions!
I think the solvent masking is not estimated correctly if only a PDB file is provided (i.e. no experimental data) to SFcalculator.
This is observable in the real space electron density (e.g if loaded in Coot).
I believe the issue is that the scales are not initialized to good enough values when data is not provided.
In
_set_scales
, currently:But at the very least kmask should be resolution dependent with some average values. The following seems to work well and gives good real space density for a few test cases:
with added resolution dependence
I use the kmask expression:
kmask = ksol * exp( -Bsol * s**2 /4)
withksol = 0.85
(midway between 0.75-0.95)and
Bsol = 250
(midway between 150-350) from Glykos & Kokkinidis, Acta Crystallogr D Biol Crystallogr. 2000 Aug;56(Pt 8):1070-2These are probably not the most representative values, but they seem to do the trick. Thoughts?
The text was updated successfully, but these errors were encountered: