Dear all,
I am getting an error message when I run arp/warp using CCP4i.
*/"QUITTING ... ARP/wARP module stopped with an error message:
RESTRAINTS
*** Look for error message in the file:
/home/rafael/MAD/CCP4/2_warpNtrace_build.last.log
[1] 11549/*
The only error message I can find on the ab
Protein crystals grown in Phosphate-Citrate buffer, pH 4.2 behave exactly the
way Richard described: they first turn blue then fade through yellow-brown.
Vaheh
-Original Message-
From: CCP4 bulletin board on behalf of Richard Gillilan
Sent: Mon 3/15/2010 2:23 PM
To: CCP4BB@JISCMAIL.
lei feng wrote:
I am wondering how to make covalent bond in coot, between a modified
substrate and regular protien residue
I can not figure out how to make the bond.
That is, perhaps, because making a bond is not up to Coot - it's a
"dictionary thing".
Have a look here:
http://www.ysb
hello everyone
I am wondering how to make covalent bond in coot, between a modified substrate
and regular protien residue
I can not figure out how to make the bond. Your suggestion is appreciated.
Lei
Computational Cancer Metabolomics Postdoctoral Position
Center for the Study of Systems Biology at the Georgia Institute of
Technology
Postdoctoral Fellowships in the Laboratory of Professor Jeffrey
Skolnick are available. Specific research areas include the Molecular
and Cell Biology of
Hi Nukri,
Since you have not mention red: enclosed are two pictures taken last week at
GMCA before and after irradiation.
several shots of 1s with 20 micron beam, unattenuated, 12.000 keV, GM/CA at
APS (23ID-B)
Protein (lipidic cubic phases): 20mM HEPES pH 6.8, 200 mM NaCl, OG, diluted
in monool
Hi Nukri,
Since you have not mention red: enclosed are two pictures taken last week at
GMCA before and after irradiation.
several shots of 1s with 20 micron beam, unattenuated, 12.000 keV, GM/CA at
APS (23ID-B)
Protein (lipidic cubic phases): 20mM HEPES pH 6.8, 200 mM NaCl, OG, diluted
in monool
>
> I have personally noticed that the blue color only appears when the pH of the
> hyperquenched solution is higher than 7 or so. I assume this is because
> solvated electrons react with protons to form their conjugate base: the
> hydrogen atom. The latter species is highly reactive as well,
Bob,
It seems you have got the correct solution or very close to. Though,
something you described are confusing.
1) Normally for normal protein crystals, you may not get fitting well
in both P222 and P212121 space groups, even if
you have pseudo-translational NCS. Based on your Rs, it see
The search terms you are looking for are "solvated electron" and "color
center" (sometimes F-center). The former term is used to describe an
unbound electron trapped in between a bunch of water molecules (which
rotate their positive poles toward it to stabilize the species), and the
latter ter
>
> Dear ccp4bbers,
>
>
> I need some suggestions regarding structure solution of fused protein
> complex.
>
> After repeatedly failing to obtain crystals of a 45 kDa protein (mostly
> a-helical) we fused the protein of interest to another protein of known
> structure which is 30 kDa is size (mostl
Two POSTDOCTORAL POSITIONs to study macromolecular complexes and signaling are open at the Department of Biomolecular Mechanisms at the Max Planck Institute for Medical Research, Heidelberg. The highly interdisciplinary department focuses on understanding reaction mechanisms using crystallographic
Hi Todd,
There are many compounds that have color centers which change color as
soon as they are exposed to X-rays. Some turn, blue, some pink, some
yellow etc. I'm not sure which one is the chameleon in your buffer but
you can bring them separately next time and we can shoot them one by
one.
Chee
Hi Todd,
I believe the blue colour is caused by free electrons produced on
irradiation (the size and shape is presumably v. similar to the beam
and the colour will not spread beyond 1 um if at 100K) and these will
be produced both in the crystals and the cryo solutions. I thought
that it w
Hello
Is there any way to calculate molprobidity score for individual amino acid
residues of a protein.
Thanks in advance
Tony,
As Ed said, DDM is not, nor will ever be cheap. However, the Anatrace
sol-grade is primarily for the early stages of a protein's isolation
and purification, but is not recommended (or intended) for
crystallization or biophysical experiments. Use their purer grade for
the latter.
Greetings,
On a recent synchrotron trip, certain frozen samples were turning a
blue upon exposure to the beam. Attached is a representative image
from the crystal-centering camera. If you take snapshots down the
crystal, you can make blue dots. Note that it also colors the frozen
solut
Dear colleagues,
I would like to draw your attention to an upcoming educational webinar
that will cover data processing with mosflm. This webinar is the 3rd in
the previously posted webinar series to cover X-ray diffraction data
processing packages.
This week's webinar, presented by Andrew L
When I deposit at the EBI the deposition software moves solvent to
assocoiate with a protein molecule. If that has been done, those
messages would mean that the solvent is indeed unconnected to anything.
It seems a bit unlikely chemically - and I would check the maps..
has something beem miss
Dear all,
A beamline scientist position is available to work on the tuneable MX
Beamline I03 (http://www.diamond.ac.uk/Home/Beamlines/MX/I03.html) at
Diamond Light Source, UK.
For more information on this position, please visit
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0555-TH.html and for
Mark J. van Raaij wrote:
apologies for that question - it IS there, two positions about space group search ("X-ray cell
dimensions"). Can't figure out why I did not see this...looking with my ears I guess...
Mark
Doesnt the oca search allow you to set both?
Eleanor
I think your crystallographic colleague is misled.
SCALEIT simply scals two or more sets of ampiltudes to the chosen one. (
labelled FPH1 FPH2 etc scaled to FP..)
It knows nothing of the contents of the asymmetric unit..
truncate uses the number of residues in the asymmetric unitr to assign a
22 matches
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