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
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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..
P
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
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For whatever obscure reason, I need to refine a model that has two
different residue types as alternate conformers with the same residue ID.
Presented with a pdb file that has such feature, Refmac fails saying this
ERROR: in chain A residue: 443
> different
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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 r
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Dear all,
In the current version of phenix.refine contains the separate option for
refinement: xyz (reciprocal space) and xyz (real space ). What does it
mean and how it differs from the previous versions which had xyz and real
space instead.
So I just wanted to know what does it actually do?
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