Re: [phenixbb] Two versions of TFZ, molecular replacement
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! -- _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb ------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: [email protected] CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Hi, I still don't have any idea why the TFZ-equivalent is so much lower than the TFZ, but the result of molecular replacement after AutoBuild against the same data set is almost meaningless. Once the structure has been refined against the data, molecular replacement will place it in the same position and it will be guaranteed to give a strong signal because it has been refined to agree with the data when placed in that position. This would be true even if the solution were incorrect! Best wishes, Randy Read On 15 Sep 2012, at 00:51, yzhao wrote:
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_...
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!
--
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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