It would not surprise me at all if pseudotranslation (aka tNCS) were holding
you back. It is like kryptonite to all phasing techniques, MR, MAD, SAD, MIR,
you name it. I recently did an analysis of old, never-solved data sets from my
beamline. These are MAD/SAD data that don't match anything
Hello folks,
I have the distinct honor of chairing the next Gordon Research
Conference on Diffraction Methods in Structural Biology (July 26-31
2020). This meeting will focus on the biggest challenges currently
faced by structural biologists, and I mean actual real-world
challenges. As much
Last time I checked phenix.refine did not use sig(F) nor sig(I) in its
likelihood calculation. Refmac does, but for a long time it was not the
default. You can turn it off with the WEIGHT NOEXP command, or you can
even run with no "SIGx" at all in your mtz file. You do this by leaving
A classic case of this is crambin. Residue 25 of 3nir.
-James Holton
MAD Scientist
On 6/24/2019 1:00 AM, Guenter Fritz wrote:
> Dear all,
>
> I am refining a multimer and mass spec data of the sample indicate
> that there is a mixture of two variants which differ in one amino acid
> residue.
The CCP4 program you are looking for is "cad". Using the "SCALE" keyword you
can apply an overall positive or negative B factor to any mtz data set.
Negative B factors are sharpening, which is what you are trying to do.
There is also another program called "ecalc", which is specifically
Has anyone ever done the experiment of switching precipitants/cryoprotectants
and verifying that this crown-of-PEG around lysine goes away when you do?
Just curious,
-James Holton
MAD Scientist
On 4/1/2019 4:26 PM, Paul Emsley wrote:
Agreed. "PG4" - so that you don't have to go searching for
In coot, select.
Validate > Difference Map Peaks > Find Peaks Above 4 r.m.s.d > [Find Peaks]
What do you see?
Always remember, the real-space representation of your Rwork is the Fo-Fc map.
The biggest peak or valley in this map is usually dominating your Rwork/Rfree.
If you feel your
10% of which beam?
-James Holton
MAD Scientist
On Feb 26, 2019, at 1:38 PM, Maria Håkansson
mailto:maria.hakans...@saromics.com>> wrote:
Dear all,
We have experienced nitril groups not present in the electron density
after data collection on compounds bound to different proteins.
In one of
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
plastic.
Plastic cover slips are no good for UV or polarization, but they are way better
than glass if you happen to want to try in-situ diffraction.
(https://doi.org/10.1107/S002188981254)
If you can't afford commercial ones, then you can always cut up some inkjet
transparency film
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