Dear Randy,
On Fri, Oct 13, 2017 at 04:11:44PM +0100, Randy Read wrote:
> Just to add to this point. The MR algorithms in Phaser are now able
> to make better use of intensity data, which is particularly
> important when you have any very weak data. Having weak data can’t
> be avoided when you
Thank to all for the replies !
I have tried the UCLA server using the unmerged intensities from XDS
and the verdict is strong anisotropy
The Rfactors (after Phaser+Refmac) are only slightly lower for the
Corrected.
Non Corrected:Corrected
R factor 0.3778 R
Just to add to this point. The MR algorithms in Phaser are now able to make
better use of intensity data, which is particularly important when you have any
very weak data. Having weak data can’t be avoided when you have serious
anisotropy (or tNCS or a combination of the two). Unfortunately,
Dear all,
this is a question about scaling data integrated in CrystalClear
(Rigaku data processing gui based on d*trek) in ccp4.
Since scaling dtprofit.ref files from different scans is sometimes poor
or even failing within CrystalClear (i.e. with dtscaleaverage after
merging them), I used to
Dear GIA,
In addition to the anisotropy, I would also check your diffraction images and
make sure that there are no (even hardly perceptible) ice rings present.
Depending on how the data processing software handled this, they may cause high
Rfactors in the range you mentioned.
Best,
Herman
Dear Gia and Paul,
about anisotropy, one point to keep in mind is that it is not
necessarily linked to the difference in resolution limits.
In fact I am at the moment working on one of these cases, with extremely
large difference in resolution limits, but relatively low anisotropy.
Anisotropy
Gianluca,
you could become an expert yourself, by trying
- the UCLA anisotropy server
- STARANISO
with these data, and report here what the outcome in each case is -
Rwork/Rfree, map appearance, ...
My personal experience is that both refmac and phenix.refine deal well with
moderate
I had a similar problem to what you describe. In my case the dataset was
severely anisotropic (2.6A, 3.4A, 4.6A in each axis). The R factors were stuck
similar to yours but the map looked good. I was told by someone with a much
better appreciation of the theory than myself that the anisotropy
Dear All,
I am trying to refine a structure at 3.3A. Model has 60% identity to the
target. Maps look OK (for 3.3A) and rebuilding in Coot is relatively
straightforward. However, after some rebuilding cycles the R factors are
stuck at 0.37/0.39 (REFMAC).
XTRIAGE tells me that everything is normal
You have labelled the TYC as an L-peptide in the dictionary have you? (
Look at any peptide for the position and format for the label ) I thought
REFMAC would then automatically creat a peptide link between residue n and
n+1
Eleanor
PS and remove the TER record!
On 13 October 2017 at 08:08,
Hi Abhisek (and BB),
I use the attached cif file. It has an NH2 residue defined as a peptide and
gets automatically linked to the peptide chain in the buster procedure I use.
So if your last residue is Tyr 100, you add NH2 101 as a HETATM in the peptide
chain.
I have not tested it with Refmac
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