And given that all these maps (Fo, Fc, and their differences)
are made without the F000 term and so have average value zero,
it is highly likely that Fc will be negative in the region
of the deleted subunit (solvent is the lowest density in the model
except for the chinks of vacuum between the atoms in the protein,
and averaging over the volume of the protein you expect protein
to be electron-denser than solvent).
If Fc is negative then Fo-Fc negative implies Fo is still
more negative, and 2fo-fc cannot be positive.
It would be instructive to make Fo and Fc maps and check
their values in the region of the deleted subunit to resolve
the contradiction.
On 10/11/2017 04:47 PM, Edward A. Berry wrote:
This is hard to understand/impossible, at least in terms of
simple 2fo-fc and fo-fc maps.
We can think of a difference map as the difference between two maps,
like fo-fc map = fo map - fc map.
There is no model in the region, since you deleted it,
so Fc=0, and Fo-Fc negative => Fo<0, so 2fo-fc cannot be positive.
No, wait, there will be solvent, so Fc = Rho(solvent)
Fo-Fc is negative, so Fo <Rho(solvent)
2Fo-Fc positive => 2Fo>Rho(solv)
2Fo > Fc > Fo
Fo > 1/2 Fc
So this would be possible if the density of your protein is less than
that of the solvent but more than half that of the solvent.
Partial occupancy? but where the protein is missing there
would be solvent (in Fo if not in Fc),
so you still couldn't get below density of the solvent.
Maybe its a problem with the solvent model?
On 10/11/2017 09:48 AM, Karsten Dreifus wrote:
Dear all,
I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu.
Molrep (template with 70 % seq identity) finds three NCS molecules
(the template model has only 1 chain as it is in different space
group). Now, REFMAC refines it to 25/30 % R/RFREE. I was just worried
about model bias, so I just deleted chain C and re-ran the refinement.
I observe that in the place of chain C, the DELFWT map in Coot shows
negative density (red colour). Shouldnt the deleted regions show
POSITIVE density (green colour)? The 2fo-fc map in the deleted region
shows usual blue colour. I shook the 2chain model with Phenix simple
dynamics and then ran refinement with same results.
How do I verify the model is correct?
Karsten
