Peter Zwart wrote:
Hi,
This can might well be due to wrong space group.
I suggest fixing the space groups by hand and running it in each
possible space group that is possible.
(P 31 2 1, P 32 2 1, P 3 2 1 are your options)
Did you run xtriage already?
P
2009/8/17 Yuan Cheng <[email protected]>:
Hey,
I am trying to use phaser to solve a protein structure. There is predicted
to be 8 mol/asu based on Matthew coefficient analysis.I am using a protein
that shares about 35% identity with my protein as a search model. Phaser
found the first five solutions and then failed to find the 6th. The LLG and
Z-score are as following. The possible loop in the chainsawed model has been
truncated.
"SOLU SET
RFZ=5.2 TFZ=7.1 PAK=0 LLG=44
RFZ=5.3 TFZ=13.8 PAK=0 LLG=169
RFZ=4.3 TFZ=69.6 PAK=0 LLG=1209
RFZ=4.6 TFZ=60.6 PAK=0 LLG=2200
RFZ=4.3 TFZ=5.7 PAK=0 LLG=2163
I used coot to check the difference map made with the model including the
above five solutions.The first four solutions fit the density very well
(didn't see many positive or negative densities). The 5th solution didn't
fit the density at all. I saw many empty density in the map, indicating I
still need to find more solutions.The space group I am using is P3 2 1.
Could this be caused by a wrong space group?
Could anyone give me some suggestions about this? Thanks a lot!
Yuan
Hi every,
Thanks a lot for your reply! Actually I am pretty confusing
here about the using of different space groups.
The.mtz file I am using now as the input file for phaser is in space
group P3. Phaser gave me the first four solutions like I mentioned in
last email, but failed at the 5th one. Then I realized there might be
something wrong with the space group or the data. I used Phenix.xtriage
to re-analyze my data (P3 space group). Merohedral twinning and
pseu-translational symmetry were found as following,
Statistics depending on twin laws
------------------------------------------------------------------
| Operator | type | R obs. | Britton alpha | H alpha | ML alpha |
------------------------------------------------------------------
| -h,-k,l | M | 0.738 | -0.137 | 0.000 | 0.022 |
| h,-h-k,-l | M | 0.047 | 0.390 | 0.429 | 0.478 |
| -k,-h,-l | M | 0.746 | -0.143 | 0.000 | 0.022 |
------------------------------------------------------------------
"The analyses of the Patterson function reveals a significant off-origin
peak that is 82.25 % of the origin peak, indicating pseudo translational
symmetry."
Also, The analysis indicates P 3 2 1 and its alternatives P31 2 1 and
P32 2 1 might be the correct space group. Then I used the Sort/reindex
MTZ fils module to change the space group to P 3 2 1. I forced Phaser to
use P 3 2 1 as the space group to search for more solutions with the
four solutions already found fixed. But I didn't get any better result.
I used phenix.xtriage to analyze the data in P 3 2 1. It indicates there
might be one twinning operator,but different tests gave different
answers.But there is still a pseudo-translational symmetry.
Statistics depending on twin laws
-----------------------------------------------------------------
| Operator | type | R obs. | Britton alpha | H alpha | ML alpha |
-----------------------------------------------------------------
| -h,-k,l | M | 0.759 | -0.152 | 0.000 | 0.022 |
-----------------------------------------------------------------
"The analyses of the Patterson function reveals a significant off-origin
peak that is 82.17 % of the origin peak, indicating pseudo translational
symmetry."
I have a couple of question now
1)Do I need go back to HKL2000 and redo the index,integrate and scale.
Since the .sca and .mtz I have now is in P3. I don't know whether the
unit cell dimension is going to change if I redo it in P3 2 1.
2)what does the pseudo-translational symmetry actually means? I don't
quite understand this concept and what should I do about it?
This is a really long email. I appreciate your attention very much.
Yuan
