Dear All:
I am refining a structure with TLS parameters in REFMAC5.
When I run the Procheck, some warning appear like below:
--- generate density ---
WARNING: Determinant(U) = 0 : -0.000475003297
for atom: C , res: 18, CHAIN: 1
U: 0.08410 0.31220 0.17130
Dear Eleanor,
Yes the native is a dimer and we did the search using the dimer as a
model but we had similar results (i.e. all programs find one molecule).
The graphs from TRUNCATE show rather normal and I am attaching a gif
file with the plot for the cumulative intensity.
As for
Dear all,
I am refining a structure in which there is an fluorine atom in the
inhibtor. When I go on the energy minimization in CNS, an unusual error
happened to this atom:
Program version= 1.1 File version= 1.1
CONNECt: selected atoms form 9 covalently disconnected set(s)
list of isolated
According to the error message your offending atom has a type:
chemical=FPAF
scatter.lib assigns scattering factors based on chemical type, and there
are ones for F and F-1 but of course not FPAF - this would likely
be the source of your problem. The quick fix is to make your own copy
of
You dont say whether the molecules in the native cell form a dimer - if
so I would search with that (you may need to turn off the packing search)
Or whether there is a pseudo translation vector in the mutant form..
Or what the data analysis graphs from TRUNCATE show - are they normal?
Eleanor
Hi Demetres,
not sure if this is going to be usefull, but here I go.
Your native has a twin law that and your cell is pseudo C222. The
mutant is not. pseudo merohedral twinning is not handled well by the
twin server you derscribe as it relies on lookup tables.
There is no obvious 'perfect'
Oh dear - this is tricky!
You could have a dimer in the asymmetric unit, or two monomers in the
asymm unit which generate dimers using the crystallographic 2 folds.
Things worth checking -
What does the self rotation show? Is there a clear 2 fold axis which is
different from the
