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