Dear Bert,
The first thing I would do is to calculate the Matthews number: Does at least
one monomer fit in the P622 asymmetric unit? If not, your crystals are
definitively twinned.
As mentioned below, I would also check the I^2/I^2 ratio, but I would do
it with the data processed in P6,
Dear Bert,
as Dirk has pointed out, if P622 is the correct space group, then the twinning
statistics printed out if you process in P6 are meaningless.
Intensity statistics, like the ratio of I^2/I^2 , can be misleading if
there is (e.g. pseudo-translational) NCS in the crystal; however, the
Hi Shane,
some crystal forms of trimeric AcrB (a multi-drug resistance secondary
transporter) have 3 (or 6) monomers in the ASU and these are substantially
different, which suggests how the protein functions.
One reference is e.g. Seeger et al. (2006) Structural Asymmetry of AcrB
Trimer
On 27 Jan 2014, at 19:08, Shane Caldwell shane.caldwel...@gmail.com wrote:
Here is another interesting one:
Perez, C., Koshy, C., Yildiz, Ö., Ziegler, C. (2012). Alternating-access
mechanism in conformationally asymmetric trimers of the betaine transporter
BetP. Nature.
best wishes,
Tobias
For reference, the CCP4 tool is called 'pdb2to3'
-- David
On 14 January 2014 18:32, Almudena Ponce Salvatierra
maps.fa...@gmail.comwrote:
Thank you all very much for your very helpful advices! I managed to solve
my problem! :-)
Best,
Almudena.
2014/1/14 Ashley Pike
Try looking into tetartohedral twinning as well--I think I may have such a
crystal, and it's tough going. And as Kay pointed out, try the various P3's.
Since I have not yet been successful in figuring my similar case out, what do
people on the list recommend as an approach to figuring this
Dont forget that with twinning in apparent point group PG6/mmm the
true SG may be P6i or P3i21
See the twinning notes: http://www.ccp4.ac.uk/dist/html/twinning.html
Detecting twinning can be problematic -
My rule of thumb, following the procedure od ctruncate::
0) Check the matthews
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Also, if you have translational NCS then recent versions of Phaser can correct
for the statistical effects and give you I^2/I^2 moment tests that are
diagnostic of twinning. This works pretty well for 2-fold tNCS (i.e. one major
Patterson peak corresponding to one or more pairs of molecules
Thank you all for the suggestions. I lowered the hash-max and could get ray
tracing to complete for line or even ribbon modes (to be honest line mode
worked even without lowering the hash-max). But as Matthew pointed out, I
could not get it to work in the cartoon mode. I think I am restricted here
Two more papers on twinning I found informative:
===
Acta Cryst. (2003). D59, 2004-2016[ doi:10.1107/S0907444903021085 ]
Twinned crystals and anomalous phasing
Z. Dauter
Abstract: Merohedral or pseudomerohedral twinning of crystals cannot be
I was wondering if anybody knows of a program or script that you can run that
will calculate local RMSDs between 2 superposed pdbs and color based on those
local RMSDs or allow for the ability to color based on RMSD? I have a molecule
that is similar in some aspects to another molecule but also
Dear Bert,
In my own review:-
http://www.tandfonline.com/doi/abs/10.1080/08893110802360925?journalCode=gcry20#.UulGyGtYCSM
molecular replacement emerged in my mind as the most robust option for
structure determination in such a case, apart from finding an untwinned crystal
form of course.
Best
Hi Tim -
There is a script on the PyMOL Wiki that does just this:
http://pymolwiki.org/index.php/ColorByRMSD.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/
On Jan 29, 2014, at 12:43
Postdoctoral Associate: Applications of Pressure to Structural Biology
The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron
Source (MacCHESS) has an opening for a post-doctoral associate to continue
development of the pressure cryocooling method (Kim et al. Acta
Dear All,
We have obtained many tiny protein crystals in a condition
containing 0.1M citric acid pH 3.5, 2M ammonium sulfate. The crystals are too
small for mounting in loops.
We intend to vary the salt concentration pH to obtain larger
crystals.
Could
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