[phenixbb] Two versions of TFZ, molecular replacement

[yzhao]

Hi,

Some information may be needed. 

The model used to do molecular replacement is not an original homolog PDB file.
I feed the homolog structure and sequence alignment to MR_rosetta, and I
obtained an overall_best.pdb from AutoBuild(diffraction resolution is about 3.
5A). 

So I use this overall_best.pdb to run Phaser, and achieved a solution as I just
mentioned. the overall_best.pdb from AutoBuild has no obvious regular secondary
structure relative to the homolog structure, but their overall appearances are
very similar.

Before I run Phaser, I also checked native Patterson, there is no large off-
origin peak. Additionally, the self rotation function and matthews_coef
indicate there is a monomer in ASU.

Thanks a lot!
--

Yan Zhao
Randy Read 写:Hi,
There's an explanation of the TFZ== entry and how to interpret the job history
on our web page:http://www.phaser.cimr.cam.ac.uk/index.php/
Molecular_Replacement#Has_Phaser_Solved_It.3F
Basically, the TFZ=13.9 means that, in the translation search using the
orientation that came from the rotation function, the Z-score of this peak was
13.9.  However, we found that the TFZ was too sensitive to random errors in the
orientation, so Phaser now computes what the TFZ score would have been if the
orientation in the translation search had been the optimised one from the rigid-
body refinement.  (We call this the TFZ-equivalent, denoted as TFZ==.)  So
after the refinement (giving LLG=235), a random sampling of translations shows
that the TFZ score would have been 5.0 for the refined orientation.  The next
two entries are the LLG after the final refinement at full resolution (239) and
the TFZ score for that refined solution (again 5.0).
What you see is very unusual behaviour.  The TFZ -equivalent is almost always
higher than the original TFZ, and I can't recall a case where it was
significantly lower.
One possible explanation occurs to me.  If your crystal has translational NCS (
indicated by a large off-origin peak in the native Patterson) and you're
searching for a dimer, a translation search with the dimer axis parallel to a
crystallographic 2-fold would give a very sudden increase in the LLG when the
dimer is in the right place relative to the crystallographic 2-fold to generate
a model that obeys the translational NCS.  Then, if the refinement changed the
orientation of the dimer so that its axis was less parallel to the
crystallographic 2-fold, that would reduce the modulation of the calculated
data and reduce the TFZ.
If these are the circumstances of your job, then you should be able to fix it
by making sure that you have a recent version of Phenix, then running a job
looking for 2 copies of the monomer.  In that case, Phaser will take proper
account of the translational NCS and there won't be any strange artefacts.
If those aren't the circumstances, then I'm very puzzled and would appreciate
receiving the data, model and other information needed to reproduce your job (
off-line) to check out what is going on!
Best wishes,
Randy Read
On 14 Sep 2012, at 20:13, 赵岩 wrote:Hi everyone,
I am trying to solve a structure though molecular replacement and I have
obtained a suspected solution.
The header of the solution as follows,

REMARK TITLE  [no title set]
REMARK Log-Likelihood Gain:  238.884
REMARK  RFZ=10.9 TFZ=13.9 PAK=2 LLG=235 TFZ==5.0 LLG=239 TFZ==5.0
REMARK ENSEMBLE 1 EULER  15.53   0.10 344.54 FRAC -0.499 -1.000 -0.499

At first sight, the solution has no problem(TFZ>8), but the second and third
TFZ are very low. 
For a correct solution, the later TFZs always higher than the first TFZ.
So I don't konw how to understand the later TFZs and what extent I can refer to
them.

Thanks a lot!

--

 


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------Randy J. ReadDepartment of Haematology, University of CambridgeCambridge
Institute for Medical Research      Tel: + 44 1223 336500Wellcome Trust/MRC
Building                   Fax: + 44 1223 336827Hills Road                     
              E-mail: rjr27 at cam.ac.ukCambridge CB2 0XY, U.K.                   
   www-structmed.cimr.cam.ac.uk



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