Hi all, I have an anisotropic native data sets with heavy atoms and I want
to use the anomalous signal for the final refinement. Does anybody know how
to run the anisotropic sharpening and output the F(+)_ISOB, F(-)_ISOB? It
seems both the anisotropy server (UCLA) and phaser_anisotropy analysis can
A *post-doctoral position* is available to study the molecular mechanism
for self vs. non-self discrimination by the innate immune system. We use a
combination of X-ray crystallography, biochemistry, cell biology and
virology to characterize structures and functions of key host molecule
Hi Jeorge:
My Luddite approach to such things:
grep -v ANISOU original.pdb > iso_only.pdb
HTH,
Bill
William G. Scott
http://scottlab.ucsc.edu/~wgscott
> On Apr 24, 2015, at 8:54 AM, jeorgemarley thomas
> wrote:
>
> Dear All,
>
> Here is the CCP4 version 6.5 installed, whe
Dear All,
Here is the CCP4 version 6.5 installed, where I want to remove the ANISOU
atoms from the pdb file, but its shows failed job with an error message :
"has failed with error message
child process exited abnormally"
So I am not able to figure it out, how to rectify. Please suggest.
Thank y
Dear all,
the lab of Hartmut Michel at the Max Planck Institute of Biophysics has an
opening for a postdoctoral scientist.
For more informations see:
http://www.biophys.mpg.de/en/open-positions/postdocs.html
Best wishes
Julia
_
Dr. Julia Preu
Dep
You could try an LLG anomalous map from Phaser as well to clarify the matter:
in my experience, even sulfurs are found, and your Rb should have f” ~0.75 even
at 1 Ang xrays. Also, you could refine in Refmac including anomalous data, and
refine occupancy of Rb.
Having both modeled into the data
Hi all,
Picture attached.
I solved the structure of a membrane protein using LCP. When trying to
identify the cation-binding site, I co-crystallized with Rb+. I see strong
density corresponding to Rb+, and it was confirmed in an isomorphous
difference map.
One problem: in the native structure I
Following up on Dave's suggestion, you could try using crystal screens as
additives. This has worked well in my lab. The idea is to mix the condition
that you currently have (the "base") with all the crystal screen reagents you
have in stock (CS, Index, etc.). As a first trial, use reservoirs
Dear Deepa,
When classifying structures you need to first ask "why?". For example, if you
want to get an idea about evolutionary relations, you must try to find their DNA
sequences and analyse those in the light of a multiple sequence alignment (MSA) that
follows the protein alignment.
In phar
Dear all,
I am Deepa, MSc final year student. For my final year project, I am working on
protein structure classification. I have a set of 300 methyltransferase
protein structures. I wish to classify the proteins in to different groups
based on their secondary structures and sequence. I have t
Along those lines suggested by David I would say these crystals are way too big.
Try freezing some when they are smaller. It would also be worth trying to
freeze in meshes to support the fragile plate instead of conventional loops.
J?rgen
..
J?rgen Bosch
Johns Hopkins Universi
There's some discussion of this in here:
http://journals.iucr.org/d/issues/2013/07/00/ba5199/index.html
section 6.5.
But basically you figure out how much dose a volume can take, and then
change collection parameters so that each volume gets that full dose.
The "strategy" is just one way to qu
Hi Mark,
I think William was asking by how much he could increase the
transmission by given a certain crystal size - the rough answer being he
could increase to 100% as he has ~10 positions given the beam and
crystal size... But a proper calculation is always better and of
course one has
Hi Matthew,
William seems to want to increase the x-ray intensity gradually during the
experiment by augmenting the transmission gradually. It that possible? If so,
would it be advisable?
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-
Dear All,
An MRC-funded PhD position (starting in September 2015) is available in my
group at the University of Leicester (UK) to target protein-protein
interactions in poor prognosis T-cell lymphomas, in collaboration with Profs
Simon Wagner and Richard Bayliss. This is an exciting opportunit
Dear William,
at the ESRF we have a Helical characterisation workflow that will
calculate a strategy based on the observed diffraction patterns and the
distance between 2 points selected on a crystal, best wishes, Matt.
On 2015-04-24 12:00, William Chao wrote:
Dear all,
Does anyone have ex
Hi,
I try to run aimless (on OS10.6, CCP4v6.5.007) using as input a xds output.
Aimless actually finishes (and scales fine), but then I get the error below
and truncate does not start:
---
/CCP4/S1_9_Kin_VSCFAKK7_6_correlplot.xmgr" ROGUEPLOT
"/Users/CSAG/Structural/PROC/2015_04_19
Dear all,
Does anyone have experience in maximising anomalous signal during a
helical/line scan? Most (all?) automated data collection strategies in
synchrotrons seem to work on a single point of a crystal but don't give
strategies for line scan. Would it be advisable to increase the recommende
Hi all, late to the discussion as usual...
Related to the issue of "why does my single point mutant appear to have
residual activity", what do people here make of this warning from 1989?
http://pubs.acs.org/doi/pdf/10.1021/ar00163a001
Some highlights:
"Substitution of the Ser68 codon with a codo
Applications are invited for a Postdoctoral Research Associate in the
laboratory of Dr. Julie Welburn, funded by Cancer Research UK. The laboratory
investigates fundamental mechanisms of chromosome segregation at the molecular
and cellular level. The focus of our laboratory is the function and
Lysine-methylation has proved to be helpful to change the molecular packing
in protein crystals (i.e. you might obtain a completely different crystal
form). _Gang
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Prerana G.
Sent: Friday, April 24, 2015 5:01 AM
To: CCP4BB@J
The crystals don't look that bad in my opinion. Maybe the cryo step is sub
optimal? Try using large loops (reduces surface tension forces during
transfer). Butane 2,3 diol is a good cryo to try. Maybe shoot them at room temp
(in situ) to get an idea of how they diffract before you manipulate the
There have been quite a few reports that the addition of a low concentration of
alcohol (e.g. isopropanol, a few %) can help to increase the thickness of thin
plate crystals like these. However, these are probably in the Hampton additive
screen that David Briggs suggested.
Good luck,
Andrew
O
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