Dear Samuel,
I'm guessing you are not constrained by sample availability. Consider a
multi-crystal approach to understand your native structure and contrast against
structures with low occupancy binders (Pearce et al 2017,
https://www.nature.com/articles/ncomms15123 ).
That structure (a
Hi,
this is why Polder map tool also includes analysis of the map in question
to determine whether it looks like bulk-solvent or something else, as
described in paragraph 5 here:
http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf
This analysis tells you in plain English what you are
Hi Fellows,
I'd really like to emphasize the point in the Buster instructions "be
careful when
examining fo-fc at low levels" when solvent is excluded. If the solvent
contribution
is omitted where you suspect the ligand (e.g. occupancy 0.02 in Refmac),
there
will be a fo contribution there from
Dear Samuel,
On Mon, Feb 04, 2019 at 11:39:58AM +, Samuel Davis (PG Research) wrote:
> I'm wondering if anyone knows if it is possible to turn off the bulk
> solvent modelling in Refmac5, for the purpose of generating Polder
> maps? I know that an option for Polder maps is directly
Yes, Dorothee is right. Don't turn off all the bulk solvent! That is not a
polder map.
In refmac you want to use the keyword:
solvent exclude DUM
And then fill the space you want to have no bulk solvent with water atoms with
residue ID "DUM" and perhaps occupancy set to zero, since you don't
The keywords are:
SCALE TYPE SIMPLE
SOLVENT NO
I always use for a completed sctructure
SCALE TYPE SIMPLE
SOLVENT YES
and then a set of 4 numbers for scale and Bfactors are output .
There is an option to give these as a FIXED SCALE.
Forgotten the exact keywords but they will be in the manual..
Hi,
Please note that for polder maps, the bulk solvent is reset locally.
Turning bulk solvent off entirely most likely deteriorates maps.
Best wishes,
Dorothee
On Mon, Feb 4, 2019 at 3:50 AM Samuel Davis (PG Research) <
s.w.da...@dundee.ac.uk> wrote:
> Hi,
>
> I'm wondering if anyone knows if
It should be according to the manual
http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#solv
If you using CCP4i, I believe this is done by unchecking the "Calculate the
contribution from the solvent region" box in Scaling section.
---
I don't know why the sacrifice didn't work. The
Hi,
I'm wondering if anyone knows if it is possible to turn off the bulk solvent
modelling in Refmac5, for the purpose of generating Polder maps? I know that an
option for Polder maps is directly implemented in Phenix, but we ideally want
to use Refmac5, as we have used it for the rest of our
