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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 <[log in to unmask]>:
>> 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