Hi,
What happens usually is that some solvent atoms are in fact closer to a
symmetry-related molecule than the one you are working on. The PDB has
programs to reposition these water molecules closer to the "correct"
macromolecule or subunit, and they will provide you with the modified
waters
Hello,
Is there a magic tool doing the job of scaling 2 MTZ to the same scale?
For the moment I know with ccp4:
rwcontents then wilson then mtzutils
with phenix:
lsq_scale (in fact I am lying, I was forced to run ccp4's cad before)
Is there a simpler way with ccp4?
As I am not a crystallograph
Hi Francois,
SCALEIT in CCP4 sounds like the tool you want - this is for scaling
e.g. native and derivitive data sets together. You will need to cad
together the two files first though.
This is illustrated in the tutorials here:
http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-ma
Dear All,
I have several proteins that share a common problem. When crystallization,
once the precipitant is PEG, the protein will be precipitated in seconds.
Even the protein concentration is just 2 mg/ml. But if the precipitant is
salt such as NH2SO4. The drop is clear for months, even high
Graeme Winter wrote:
Hi Francois,
SCALEIT in CCP4 sounds like the tool you want - this is for scaling
e.g. native and derivitive data sets together. You will need to cad
together the two files first though.
My crystallographer colleague tells me that if we use
scaleit there is a risk if there
Hi Francois,
As I understand this, they (the F's) should be already on an
"absolute" scale as determined by the Wilson stats as TRUNCATE does
this scaling. What SCALEIT does is to scale the data sets together in
terms of an overall (or anisotropic) temperature factor and overall
scale, so that the
Have you ever tried the condition of AS as precipitant and PEG as the
additive? They have opposite functions on your protein's solubility:one
increases and decrease it. Maybe you can vary the ratio of them to
control your protein's solubility. And the xtals may be seen in some
conditions.
Go
Hi,
I am trying to soak some sugars in my crystals, but the cystallization
condition has a pH of 4.0. Does anybody has any experience with acidic
oxidation in such a case. I think I can´t avoid oxidation at this pH? Any
suggestions, or do I have to screen for other conditions?
Thanks,
P.
Hi,
I have soaked various crystals at that pH with various sugars and
never had a problem with oxidation of the sugar. I wouldn't worry
about it. What group do you think will be oxidized?
Nat
On Fri, Mar 12, 2010 at 5:35 AM, Paul Lindblom
wrote:
> Hi,
>
> I am trying to soak some sugars in my
Dear all,
in the process of pdb file deposition, after some error removal,
suddenly pdbdep made errors on the "covalent bond angles" of all PRO
residues.
Does any one has any suggestion? :(
Regards,
Azadeh
A postdoctoral position is available for a skilled protein crystallographer
interested in challenging projects in the Hurley lab, NIDDK, NIH. We are
seeking to understand the structure and function of membrane-associated
multiprotein complexes involved in protein and lipid trafficking. Some of
the
Dear All,
In every refinement round the wxc and wcu are out of control, although I
modify the def file and change the values of wxc=1 and wxu=1 so they
are tightly restrained, but it failed to fix the problem, wxc and wxu
values keep fluctuating, in my latest refinement round wxc=256!! wxu=3.
T
Could you transfer your crystals in a higher pH buffer?
Maia
Paul Lindblom wrote:
Hi,
I am trying to soak some sugars in my crystals, but the cystallization
condition has a pH of 4.0. Does anybody has any experience with acidic
oxidation in such a case. I think I can´t avoid oxidation at this
Yes Im using wxc_scale and wxu_scale but I also use tls refinement,so in
this case if the weights need to be tightly restrained, I should not use
tls refinement!
**
Mohd A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research building,Rm 331
4500 San
Hello,
I am looking for an inexpensive US source for large quantities of
dodecylmaltoside. Can anyone help me?
Thank you!
Computational Systems Biology Postdoctoral Positions
Center for the Study of Systems Biology at the Georgia Institute of
Technology
Outstanding Postdoctoral applicants are sought in Computational
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You get what you pay for, and this is not a cheap detergent!
If your application is not sensitive to a little bit of the alpha- anomer,
try Anatrace sol-grade, 25 g for $803.01:
http://www.affymetrix.com/estore/browse/brand/anatrace/product.jsp?productId=131630&categoryId=35662#1_1
If you find som
Which version did you use? I remember the old version of phenix (1.3)
will automatically change your setting (wxc and wxu) each round. And
v1.5 will automatically choose wxu if you use tls. I haven't tried 1.6
yet. Maybe there are some bugs associated with it?
The default wxc is 0.5 and wxu is 1. S
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