[phenixbb] phaser MR

Randy Read rjr27 at cam.ac.uk
Fri Jul 24 01:58:23 PDT 2009


If you're unlucky, a combination of pseudo-symmetry and twinning gives  
only weak indications of twinning, because the twin-related  
reflections are correlated but the twinning tests assume that they are  
not.  It might be worth considering that possibility.  You could try  
solving the structure in lower symmetry space groups to see whether  
you get a solution that does not exactly obey the higher symmetry.

Are you really certain about the space group?  If one symmetry  
operator is wrong (e.g. a 2-fold instead of a 2-fold screw), some of  
the symmetry operators are still right, and you can get an apparent  
solution that partly explains the data.  It might be worth running  
tests in all the variants of P422 as well.

Best wishes

Randy Read

On 23 Jul 2009, at 22:54, sbiswas2 at ncsu.edu wrote:

> Hi Francis,
> Thanks for your response. The matthews coefficient suggests two  
> molecules
> in the AU. Phaser also finds two molecules. I ran the dataset through
> phenix xtriage it did not indicate twinning though. The molecule also
> exists in nature as a monomer.
> Shya
>> Twinning? What's your matthews coefficient say? Do you know if your
>> structure is a multimer (biochemistry, etc)? Does  it agree with the
>> matthews coefficient?
>> If the unit cell is  not big enough to hold all of the contents,then
>> this is an indicator for twinning .
>> FR
>> On Jul 23, 2009, at 3:09 PM, sbiswas2 at ncsu.edu wrote:
>>> Hi all,
>>> I was trying to solve a structure by molecular replacement. I scaled
>>> the
>>> data in P4222 space group (resolution 2.7A) with two molecules in  
>>> the
>>> assymmetric unit (molecule A and B) I ran phaser with my model and
>>> got a
>>> Zscore of 5.1. When I look at the map that I got from phaser I could
>>> easily see good electron density for both molecules, However upon
>>> inspection of the electron density map there were considerable
>>> interaction
>>> or clashes with molecule B and a symmetry atom. Molecule A had no
>>> clashes
>>> however with the symmetry atoms. I was wondering if anyone knows how
>>> to
>>> resolve this.  Could it be a problem of space group. The statistics
>>> are
>>> good for space group P4222 and the I/sigI was good till 2.7A.
>>> Any advice is appreciated,
>>> Shya
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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