You mention that your Rsym is 0.6 - this seems outrageously high (except if the
0.6 is just for your outer resolution bin). If 0.6 is indeed the overall Rsym
you have a basic problem of unit cell and space group assignment to reconsider.
Check if your processing accounts for all spots and check
There isnt much evidence for twinning that I can see. Moments sensible,
Ltest sensible for untwinned data, some distortion of the cumulative
intensity plot but that could be due to integration problems.
Comparing Rfree in P3 is only proper if you have kept the same FreeR set
as you assigned
Have you used pointless to examine possible spacegroups? It is possible
to get one lattice point out and get a very high rsym
pointless will check these possibilities for you
The cell could be this:
C m m m 39.6 149.9 18.2 89.9 90.0 90.0 0.10 [-k,-k-2l,h]
You need to go back to
Hi,
I am refining a protein complexed with a modified DNA(cordinates
obtained from published structure) with CNS. But I am stuck with the pdb
format problem. I followed the tutorial on CNS website and the first
step just went wrong when command 'fix_dna_rna' didn't work. I also
tried the normal
Dear all,
I can get large amounts of a protein that is purified from inclusion
bodies. The protein is solubilized using 6M urea and refolded by dialysis.
However, treatment with urea is known to modify proteins
(N-term/Lys/Arg), which could ultimately effect crystallization.
Is this
Try first to give it a shot and see if you get crystals without too much hassle
and expense. I would recommend a size exclusion chromatography step after
refolding and from that collect a uniform sample for crystallization.
Poul
On 12/07/2010, at 13.39, meindert lamers wrote:
Dear all,
I
However, treatment with urea is known to modify proteins (N-term/Lys/Arg),
which could ultimately effect crystallization.
Is this something that people generally worry about?
For example
-would you bother cleaning up the urea by ion exchange
-get ultra pure urea (ultra $$$)
-change to
Dear all,
Since a couple of weeks, and I believe the update of my machine to Ubuntu
10.04 Lucid Lynx 64, I'm experiencing problems with the ccp4i job status.
For some reasons it cannot update to FINISHED status even if the job works
out fine. The update to version 6.1.13 didn't succeed.
Pasted
Hi Hongjun Yu,
In CNS you need to change the name of the DNA base like this:
DG - GUA
DC - CYT
DT - THY
DA - ADE
and for the thymine make sure to change the atom C7 into C5A
and it should work with CNS.
Good luck,
Pierre
Pierre Aller Ph.D.
Postdoctorate Associate
University of Vermont
Dear Sebastien,
A first guess is that the script is only familiar with english dates.
You could try to type
export LC_ALL=C
in the terminal just before you start ccp4i from that same terminal to see if
that improves anything.
This syntax is correct for POSIX shells (bash, ksh, zsh,...). In
Given your unit cell parameters + high Rsym I'd say you have an indexing
problem. If you try P2, what happens? I suspect that you might have
something as simple as incorrect beam center position and while
integration works, scaling fails (the only way you are getting away with
it is by choosing
Postdoc: Protein Biochemistry, Protein Crystallography and Drug Discovery
We hare recruiting a Postdoctoral Associate in the area of nuclear hormone
receptor biology and structural biology to join the Rastinejad lab at the
SanfordâBurnham Medical Research Institute in Orlando, Florida. The
For all those who asked about the new edition of the Sherwood book, it
is available for pre-order on Amazon (at least on the UK version,
search for Crystals, X-rays and Proteins: Comprehensive
Crystallography).
Simon
PS Jon - do I get a commission?
On 12 Jul 2010, at 11:28, F.Xavier
The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for
researchers and students interested in structural biology. At its center is the PDB archive – the
sole international repository for the 3-dimensional structure data of biological macromolecules.
Dear Users,
The deadline for Sep/Oct 2010 Collaborative
Crystallography proposals will be *July 15, 2010. *
Through the Collaborative Crystallography Program (CC) at the
Advanced Light Source (ALS),
Dear All,
July 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal
cycle.
All Berkeley Center for Structural Biology(BCSB) beamlines are equipped
with ADSC Q315/Q315R detectors, automated sample changers and data
collection software enabling high-throughput crystal screening
I just compiled the latest coot (0.6.2-pre-1.3011) on 64-bit Lucid (it
appears that the gtkglext issue is gone). I don't know what you mean by
so many compiling issues. Are you using autobuilder script?
On Sun, 2010-07-11 at 12:28 -0700, Michael Hothorn wrote:
Hi,
can someone point me to a
Hi All,
I have two different datasets of the same protein, for example dataset A and
dataset B. I want to make a difference map of [ Fo (of set A) - Fo (of set B)].
(I'll use phases of another solved structure from an isomorphous crystal). For
this I'll have to scale two different mtz files
Sorry for the clutter: This is of course for the Aug/Sept cycle.
P
2010/7/12 Peter Zwart phzw...@lbl.gov
Dear All,
July 15, 2010 is the deadline for the March/April 2010 Rapid
Access Proposal cycle.
All Berkeley Center for Structural Biology(BCSB) beamlines are equipped
with ADSC
Hi Subhangi
phenix.fobs_minus_fobs_map
will compute this map for you.
Usage examples:
phenix.fobs_minus_fobs_map f_obs_1_file=data1.mtz f_obs_2_file=data2.sca
f_obs_1_label=FOBS1 f_obs_2_label=FOBS2 model.pdb
phenix.fobs_minus_fobs_map f_obs_1_file=data.mtz f_obs_2_file=data.mtz
you can combine the two merged datasets with CAD and scale them together with
Scaleit: see ccp4i - Experimental phasing - Data preparation - Combine
datasets with CAD, Scale and Analyse datasets
Or you could give the unmerged files different dataset names, combine them in
Pointless and scale
Dear All,
I apologize for the not strictly crystallography-related query.
I am currently purifying several membrane proteins solubilized in
fos-cholines detergents and I consistently observe a significant loss of
protein at the binding step (done in absence of imidazole). Has anyone else
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