Dear Allister Crow,
in cases like these, I would recommend to apply the Babinet bulk solvent
correction instead of the mask bulk solvent correction as a control
(Refmac5 -> Scaling -> Use Babinet scaling; uncheck "Calculcate the
contribution from the solvent region"). The Babinet bulk solvent
correction only uses two overall scaling factors and is usually simple,
robust and, in my experience, does not show any local difference density
artefacts. The mask bulk solvent correction is more powerful, but,
depending on the project and the various mask radii for generating and
shrinking the mask, could produce false positive or negative difference
density. To exclude these cases, you can always calculate the Babinet
bulk solvent correction as a control.
Best regards,
Dirk.
Am 16.04.12 12:37, schrieb Allister Crow:
Board members,
I have a couple of questions regarding how to improve the solvent model as
applied to solvent-filled cavities inside proteins.
I am currently nearing the end of refinement of a protein structure at 2.8 A
resolution. I recently switched Refmac versions, upon doing this I noticed a
modest improvement in R factors, but I also notice some new features in the
difference maps. These features don't show up in the sigma-weighted 2Fo-Fc
maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the
appearance of these features (which are all located in solvent channels within
cavities inside the protein) are probably due to some difference in how the
bulk solvent contribution has been applied.
I've attached a picture of one such feature showing the difference between
Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using
the same model and refinement parameters).
My questions are therefore:
1) has something substantial changed in the bulk solvent treatment between
Refmac versions 5.5 and 5.6?
2) How can I go about changing the bulk solvent treatment to better account for
solvent contribution inside the protein cavities?
Best wishes, and thanks in advance for all your help,
- Allister Crow
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Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
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