A postdoctoral research post is available within my research group in the
Department of Biochemistry at the University of Leicester. The position is
funded by the Biotechnology and Biological Sciences Research Council and is
available from 1st September 2014 for three years.
The aim of the proj
On Tue, Jul 1, 2014 at 3:10 PM, Katherine Sippel wrote:
> My google-fu has failed me once again so I am turning to the collective
> knowledge of the bb. I'm working on a blobology challenge at the moment and
> have hit a wall. Is anyone aware of an ion that coordinates to lysine and
> prefers oct
>… I manually attempted chlorine but the density said no.
How did the density say no? Too much, too little…? I guess the bonds are too
short anyway.
What about anomalous signal using the awesomely-sensitive LLG maps from Phaser?
Depending of course on resolution, Cl- can be quite visible, if orde
We are seeking highly motivated postdoctoral fellows to join the Biosynthetic
Enzymes Laboratory at the University of British Columbia in Vancouver, Canada
(https://www.chem.ubc.ca/katherine-ryan). We are a dynamic group of researchers
working at the interface of chemistry and biology. Our goal
Hi all,
My google-fu has failed me once again so I am turning to the collective
knowledge of the bb. I'm working on a blobology challenge at the moment and
have hit a wall. Is anyone aware of an ion that coordinates to lysine and
prefers octahedral geometry. The mystery ion seems to have perfect
o
A postdoctoral research post is available within my research group in the
Department of Biochemistry at the University of Leicester. The position is
funded by the Biotechnology and Biological Sciences Research Council and is
available from 1st September 2014 for three years.
The aim of the pro
Dear Gajanan,
areaimol analyses the solvent accessible areas. It is part of ccp4, so it comes
with a window.
Best,
Tim
On Wed, Jul 02, 2014 at 12:19:50AM +0530, Gajanan Arbade wrote:
> Hello,
>
> Am working with some DNA binding proteins. If I want to calculate the buried
> surface area, whic
Hello,
Am working with some DNA binding proteins. If I want to calculate the buried
surface area, which software tools should i use? Suggest me some windows based
programs to solve my purpose.
Thank you & Regards,
Gajanan
__
Gajanan K Arbade
Research
Dear all,
Sorry for the off-topic post but would anyone here have any experience with
the new MacPro's for crystallography including using them for stereo
(passive) ? If so, would you mind sharing your thoughts and the hardware
configurations ?
Thanks very much.
Best regards,
Anirban
Dear Maher,
as far as I understand, the anomalous scattering comes from inner shell
electrons, not the valence electrons. So while you might notice a slight shift
in the peak wavelength, the strength of the signal will only reduce if you
crystal order suffered over time, but not from any oxidation
I think the ref below may be exactly what I am looking for--thanks everyone for
your help. Even when the tips were not exactly what I needed, I learned about
many tools out there which I may use some day. Generally, I am always impressed
by the collegiality and readiness-to-help of all of those
Hi everyone,
Would anyone know for how long Selenomethionine derivative crystals are
good if kept in plate at RT. In other words, would SE loose its scattering
properties due to oxidation over time? I have SElmet crystals that have
been lying in a plate for 2 months by now so I was wondering if th
You should try X-ray fluorescence measurements on your crystals
You'll see directly the presence of Zn or Ni
You can also perform a data collection at energies at both sides of max f" for
Zn and Ni.
-
Christine Cavazza
iRTSV/Laboratoire de Chimie et Biologie des Métaux
CEA Grenoble
17 rue des
Dear Dhanasekaran Varudharasu,
you won't be able to distinguish between these two metals with CuKa radiation.
You should get access to a synchrotron and collect data 1.4A and 1.25A in
addition to the CuKa set you already have
(see http://skuld.bmsc.washington.edu/scatter/AS_form.html).
The CuKa
Dear Dhanasekaran,
I am not sure from your email whether is important for you to resolve this
ambiguity with crystallographic techniques. If not, an easy and simple way
would be to shoot your crystals at energies above the Zn absorption edge (which
is at highest energy of the two metals) and th
If you have a access to a synchrotron you can try double difference anomalous
DDANO maps see Than et al. Acta Cryst. (2005). D61, 505–512 for an example
Best
Roberto
On 1 Jul 2014, at 16:10, Dhanasekaran Varudharasu
mailto:dhana...@gmail.com>> wrote:
Dear all,
I have solved a s
It is difficult! Ni & Zn are rather interchangable..
You dont say what resolution you have: There will be a small difference in
the number of electrons you expect to see at the metal site, depending on
whether it is Zn Zn2+ etc etc, and you can correct that to take account of
the f' as well.
So
Dear all,
I have solved a structure (using molecular replacement) of
metallo-enzyme which may have Zn or Ni at its active site. I collected
data at in-house CuKa radiation. Now, I am able to locate the active site
metal ion preciously but I am not able to differentiate whether it i
Keep on using the master file.
Refmac "corrects" the observations in a few ways
The overall anisotropic B correction is always applied
In the worst case scenario where you are refining considering twinning the
2FP2 output is no longer the observed FP but one after a detwinning
correction..
So
Using the "master mtz file" (as you call it) is the safe thing to do.
If you use the previous refmac output file, you have to careful the right
structure factor columns are selected. They should be non-modified by the
previous refmac run, otherwise you are refining both the data and the model.
M
Hi Dilip,
You've been doing the right thing. Just keep at it.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Dear CCP4bb users and Refinement experts,
As input for (n+1)st run of refmac, should I use as input reflection file
the output produced by refmac in the nth run? Currently I have been giving
the master mtz file as input for all runs.
I would appreciate the clarification from the community.
Hi Maher,
The message is output from crunch2 and indicates it can not find peaks in
its patterson function calculation. I would suggest to try using shelxc/d
(you can do this within crank or other pipelines) and inputting a high
resolution cut-off in substructure determination at 5.1 Angstrom and
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