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Dear Nicholas,
for a data set with 5132 unique reflections you should flag 10.5% for
Rfree, otherwise you could as well drop Rfree completely and use the
whole data set for refinement. At least this is how I understand Axel
Brunger's article about
This Ltest certainly doesnt look twinned.
But your R factors are indictive of mostly correct but still problems.
Didnt someone suggest running Arp-Warp to rebuild the structure?
This might reinterpret any dodgy bits.
Eleanor
On 10/14/2011 02:52 AM, 王瑞 wrote:
After L-test,the result are
Dear Gerard,Tom and Bernhard,
Thankyou for highlighting the IUCr Diffraction Data Deposition Working
Group and Forum.
Dear Colleagues,
I am travelling at present and apologise for not replying sooner to
the CCP4bb, and also am with intermittent email access until later
this week when I 'return
In fact, just estimating ORGX and ORGY from the first frame, using adxv or
XDS-viewer, seems to do a good job.
The silver lining of having ice (or any other kind) rings is that one can
determine the origin rather accurately by just finding the center of these
rings.
Cheers,
N.
Ruslan
I think that we are using the test set for many things:
1. Determining and communicating to others whether our overall procedure
is overfitting the data.
2. Identifying the optimal overall procedure in cases where very different
options are being considered (e.g., should I use TLS).
3.
A solution is provided by Mark.
Thanks a lot, Mark!
Best,
Xavier
Mensaje original
Asunto: Re: [ccp4bb] Fwd: Postdoctoral vacancy in Barcelona
Fecha: Mon, 17 Oct 2011 17:50:39 +0200
De: Mark J van Raaij mjvanra...@cnb.csic.es
Para: f...@ibmb.csic.es
Hola Xavi,
Hi there!
I got crystals from some synthetic peptides I bought, they are 30
residues long and are supposed to form a coiled coil. I collected
various data sets (home source, Brookhaven and Diamond), including some
at the resolution of 1.65 A, for which the space group appears to be
Yes, Rsleep seems to be just the right thing to use for this:
Separating model optimization and model validation in statistical
cross-validation as applied to crystallography
G. J. Kleywegt
Acta Cryst. (2007). D63, 939-940
Practically, it would mean that we split 10% of test reflections into 5%
If for example your presumed coil is differently bent than your search
probe, overall rmsd is high and MR will likely fail. But maybe ARCIMBOLDO
with helix fragments might do at 1.65A? George or Isabel will have a better
answer.
Good luck, BR
PS: And may San Matheus de las Coefficientes listen
Did you check for twinning? The most radical approach is to reprocess
in P1 and see what R-values you get
On Mon, 2011-10-17 at 15:09 -0200, Napoleão Valadares wrote:
Hi there!
I got crystals from some synthetic peptides I bought, they are 30
residues long and are supposed to form a
On Mon, Oct 17, 2011 at 10:09 AM, Napoleão Valadares n...@ifsc.usp.brwrote:
I have tried A LOT of Molecular Replacement using Phaser and Phenix
AutoMR. I'm using a 80% identity coiled coil helix as search model. The
programs give me solutions with reasonable maps, but it is never possible
The programs give me solutions with reasonable maps, but it is never
possible to refine to achieve Rvalues below 0.40.
This strongly suggests a space group issue.
If the systematic absences are compelling, you should try to drop it down to P2
first. Look at your packing in the C222(1). If
I should have said not compelling.
James
On Oct 17, 2011, at 12:40 PM, James Stroud wrote:
The programs give me solutions with reasonable maps, but it is never
possible to refine to achieve Rvalues below 0.40.
This strongly suggests a space group issue.
If the systematic absences are
Hi,
I agree that Arcimboldo is a good idea, especially at such good resolution
(assuming your space group is correct, an issue that others have commented on).
But you could also try, directly, something that Isabel Uson has pointed out
about molecular replacement with helices in Phaser. For
Hi, we got around to switching to ccp4 version 6.2.0, but now buccaneer
fails from the GUI. Below is what shows up if you view the com file
before execution; and below that the logfile.
Seems to me it's using the wrong python executable; the first one on my
path is certainly nothing to do
Dear PDBe users and depositors,
Due to essential maintenance of the computers in the campus data centre this
coming weekend, all web, ftp and e-mail services of the Protein Data Bank in
Europe (PDBe; pdbe.org), as well as most other EBI services, will be
unavailable from Friday 21 October 11
Seventh International Workshop on X-ray Radiation Damage to Biological
Crystalline Samples will be held at the Diamond Light Source, UK from 13:00
March 14th to 13:00 March 16th 2012.
This series of workshops was originally concerned with the effects of radiation
damage during investigation
Modeling Conformational Ensembles of Proteins and Complexes
A post-doctoral position with a focus on modeling conformational ensembles of
proteins and complexes is available immediately in the Structural Genomics
Division of Stanford Synchrotron Radiation Lightsource at the SLAC National
Pfizer Worldwide Research and Development La Jolla, have two open positions for
talented and creative research scientists in the Structural Biology Group,
Department of Cancer Research Chemistry. The successful candidates will have
significant experience in a number of sub-disciplines of
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