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 the solvent that is there.
Particularly if that solvent is a
dense solution, that fo component will show up nicely and at not so low
difference
map levels, and in the shape of that 'excluded' ligand.
Figure 2 in link illustrates that.
https://febs.onlinelibrary.wiley.com/doi/epdf/10.1111/febs.14320
If you start to fill that void with multiple ligands of various low
occupancies, you
are effectively modelling disordered solvent. This is particularly tempting
because
I found multiple cases where the classical RSR and RSCC measures give
acceptable stats for such models. The hunt for low occupancy ligands then
quickly
becomes murky density fishing business...
Best, BR
-----Original Message-----
From: CCP4 bulletin board <[log in to unmask]> On Behalf Of Clemens
Vonrhein
Sent: Friday, February 8, 2019 09:53
To: [log in to unmask]
Subject: Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to
generate Polder maps?
Dear Samuel,
On Mon, Feb 04, 2019 at 11:39:58AM +0000, 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 implemented in
> Phenix, but we ideally want to use Refmac5, as we have used it for the
> rest of our refinement and want to keep it consistent if possible.
And if you want to try the original implementation of the underlying idea as
an alternative, have a look at the ligand detection mode and maps [1]
produced by BUSTER [2]. See also [3] and some early examples of their
usefulness [4-5].
Cheers
Clemens
[1] https://www.globalphasing.com/buster/wiki/index.cgi?LigandDetectionModes
[2] https://www.globalphasing.com/buster/
[3] Vonrhein, C., & Bricogne, G. (2005). "Automated Structure
Refinement for High-throughput Ligand Detection with
BUSTER-TNT". Acta Crysta A61, C248.
[4] Thoma, Ralf, et al. "Insight into steroid scaffold formation from
the structure of human oxidosqualene cyclase." Nature 432.7013
(2004): 118.
[5] Ekroos, Marika, and Tove Sjogren. "Structural basis for ligand
promiscuity in cytochrome P450 3A4." Proceedings of the National
Academy of Sciences 103.37 (2006): 13682-13687.
--
*--------------------------------------------------------------
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park
* Cambridge CB3 0AX, UK www.globalphasing.com
*--------------------------------------------------------------
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