I think Goodhart's Law applies here (see the Wikipedia page):
When a measure becomes a target, it ceases to be a good measure.
From memory I believe Randy Read and George Sheldrick have commented that
Ramachandran plots are a good measure of structure quality, and therefore should
not be used expl
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On 25/02/15 18:08, Michael Murphy wrote:
Does anyone know of a way to adjust Ramachandran angles so that they
fall within the preferred range? Either in Coot or possibly some
online server? I have been trying to do it manually without much
success, I was wondering whether there might another wa
Dear Roberto,
I think you should try different special orientations of your crystals
in the loop to find the one in which the measurable reflections stay
away from the slow moving region (usually aligned with the beamstop
holder, so horizontal in your image), in which reflections cannot be
ac
Gyan,
With the addition of DTT to remove the skin, did you see an increase in the
resolution with the skin no longer present compared to with it still there?
-Adam
> On Feb 25, 2015, at 11:15 AM, Gyanendra Kumar wrote:
>
> Adding DTT in your protein buffer or crystallization solution may
I'm sorry, I read your reply too hastily. You are talking about adjusting weights for the
restraints we already use, not dihedral restraints. By improving the structure you will
improve the Rama score, and not the other way around. Outliers flag their residues for
inspection in case of errors s
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Hi Ed,
I'm not saying you should restrain to Ramachandran torsion angles; neither
Refmac nor pdb_redo does that. Other restraints influence the Ramachandran plot
immensely and you should optimize the weights on those (to optimize the free
likelihood, not some Ramachandran score). The typical di
Hi Almu -
It's actually even easier than what Vincent wrote as well. :) You don't need
to create multiple objects or worry about backbone selections--PyMOL has some
built-in settings that will do this for you.
# the PDB from your example
fetch 3bwp
# color however you like
color blue, resi
If you use restraints to fix outliers, I strongly suggest to refine to convergence without
restraints after they are "fixed". If some outliers return, and "% favored"
decreases, so be it.
For one thing, depositing a structure with dihedrals restrained gives an unfair
impression of higher quali
Hi Michael,
This depends a bit on how bad your backbone torsion angles are and why.
Refining with good restraint weights and flipping the odd peptide can help a
lot. If you have really low resolution you might need specific restraints. You
can try the PDB_REDO webserver at http://xtal.nki.nl/PD
Does anyone know of a way to adjust Ramachandran angles so that they fall
within the preferred range? Either in Coot or possibly some online server?
I have been trying to do it manually without much success, I was wondering
whether there might another way to do it. -Thanks
Adding DTT in your protein buffer or crystallization solution may also help.
You could try increasing amounts of DTT/BME/TCEP in your crystallization
solution and find a balance between reduction of skin formation vs getting
crystals.
Adding 2mM DTT in my protein buffer helped me get rid of much o
Dear Almu,
very easily:
#load the same pdb twice and give it two different names:
load xx.pdb, molA
load xx.pdb, molB
# show one as cartoon, the other as sticks:
hide everything
show cartoon, molA
show sticks, molB
#hide the backbone sticks of molB
hide sticks, molB and name c+n+o (this is for
Dear Ulrike,
you could try avoid the drop-air interface by overlying sitting drops with
silicone oil or a 50/50 silicon/paraffin oil mixture. Note that this will alter
the kinetics with which your drops reach equilibrium, and hence may alter your
ability to get crystals of the protein. Batch c
Have you tried crystallising in microbatch format, i.e. under oil?
I've had success with this method for exactly the problem you describe.
Regards.
Antony
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> On 25 Feb 2015, at 08:39, Ulrike Demmer wrote:
>
> Dear crystallographers,
>
> I am trying to c
Dear crystallographers,
I am trying to crystallize a soluble protein which tends to form aggregates.
The crystallization condition is 20% PEG 3350 + 0,2 M Na-Formate. During the
crstallization process a thick skin is formed on top of the sitting-drops. As
well the crystals are buried in precipi
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