Dear Colleagues,
The Protein Crystallography Station (PCS) is a high performance neutron
beamline located at the spallation neutron source at the Los Alamos Neutron
Science Center at Los Alamos National Laboratory. The PCS has a long-standing
history of serving the neutron crystallographic comm
===
SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS
===
Proposal application deadline: Sunday, June 15, 2014
Periods:
September 1, 2014 - Decemb
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(Pacific) Northwest Crystallography Workshop
http://oregonstate.edu/conferences/event/nwcw2014/
June 20-22, 2014
Summer is fast approaching and so is the Northwest Crystal-
lography Workshop to be held here
Dear Carles,
it used to be the case (and probably still is) that you had to specify
BRESID false
when using tlsanl with a PDB file from refmac5. It seems that 'TLSOUT
ADDU' specified for refmac5 allows you to use tlsanl with its default
value 'true'.
The incorrect mixture might lead to an artifi
Carles,
a few points to consider:
- you might be comparing B-factors coming from local atomic vibrations
alone (residual B, or whatever it's called), and the total atomic B-factor,
that includes all components: Btotal = Btls + Bresidual +... . (for
comprehensive review on this topic see: TLS from
TLS in phenix does seem to lead to high B factors in some of our cases.
To check whether it was particular to our datasets , we rerefined some
similar structures to ours from the PDB and found that their B factors
increased to high values similar to our structure when run through the
same phen
On Thursday, 05 June, 2014 17:51:33 Carles Palanca i García wrote:
>
> P { margin-bottom: 0.21cm; }
>
>
> Hello,
>
> I'm almost done refining a protein-DNA
> complex at 3A, but when I apply TLS (Refmac+TLSanl to include the
> ANISOU component) the B factors increase from 50-60 to 100-110
Postdoc and PhD positions in Structural Biology
A postdoc position and three PhD positions are available in the laboratory of
Prof. Eva Wolf at the Johannes Gutenberg University (JGU) and Institute of
Molecular Biology (IMB) in Mainz, Germany.
The Wolf group is currently located at the IMB
(w
P { margin-bottom: 0.21cm; }
Hello,
I'm almost done refining a protein-DNA
complex at 3A, but when I apply TLS (Refmac+TLSanl to include the
ANISOU component) the B factors increase from 50-60 to 100-110 A2.
The crystal is a bit special since it has 80% of s
George,
Remember that scattering from every point in the cell contributes to every
reflection; the R-value is a global metric of agreement between the model and
the data. Hence, calculating the R-value for a few selected residues is not a
sensible thing to do, unless you want to ask how well yo
On 05/06/14 16:10, George Devaniranjan wrote:
Hi,
First off I am pretty new to CCP4/X-ray crystallography so please bear
with me as I try to explain my question.
I was looking at a protein structure from the PDB (let's say 1aho.pdb).
I have the corresponding MTZ file. I wanted to calculate t
Hi George,
The R-factor is an overall disagreement statistic, it can not be broken down in
parts for bits of the structure.
(in other words, you can not correlate parts of the model with a subset of the
reflections in the mtz, as a non-crystallographer might think - all the
electrons in the as
Dear all,
Diamond Light Source will be holding the next training day for MX BAG Users on
Tuesday 15th July and Wednesday 16th July 2014.
The aim is to provide MX users with sufficient training to be able to operate
any of the Diamond MX beamlines efficiently and to get the most benefit from
the
Hi,
First off I am pretty new to CCP4/X-ray crystallography so please bear with
me as I try to explain my question.
I was looking at a protein structure from the PDB (let's say 1aho.pdb).
I have the corresponding MTZ file. I wanted to calculate the R-factor for
some selected residues (lets say 1
There are cases of different crystal forms of the same thing turning up
with similar lattice dimensions...
But if if the cell dimensions are the same, and one form is P4i with 4
molecules in the cell, and just enough space for one mol/asymm unit, and
the 2nd form is I422 then isnt the asymm volume
Dear Almudena,
i think your problems com from the Flag in your input.mtz . You have to check
if your mtz has the correct column name. And you have to designate the one
which correspond to PHIB.
It depend from which programm com your input.mtz .
Hope to help.
Nicolas
___
Dear all,
I am trying to get a sharper map with RESOLVE in Phenix and I provide the
.mtz or high resolution data as well as the mtz corresponding to
experimental data. However I get the following message, and I don't really
know how to fix it even though it looks quite silly. Might be that today I
Doctoral student in molecular biophysics
Type of employment: Limit of tenure, Four years
Extent: 100 %
Location: Department of Chemistry, Division of Biochemistry and Structural
Biology, Lund
First day of employment: 2014-10-01
Research assignments
The PhD student will work with structural st
Or, if for whatever reason sphere refine isn't an option, fix the metal and all
of its ligands
Sent on a Sprint Samsung Galaxy S® III
Original message From: Paul Emsley
Date:06/05/2014 3:51 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] metal ion
dominatin
On 05/06/14 08:27, Dean Derbyshire wrote:
Hi all, I recall there was a post a while back, but silly me can’t
remember the details –
How does one stop metal ions dominating real space refinement in COOT?
sphere refine?
Paul.
Hi all, I recall there was a post a while back, but silly me can't remember the
details -
How does one stop metal ions dominating real space refinement in COOT?
D.
Dean Derbyshire
Senior Research Scientist
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Box 1086
SE-141 22 Huddinge
SWEDEN
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