Dear Yuan, If the first solution is right by looking at the density. Then you can search the others by fixing the the first solution. This will accelarate your searching accuraty. Or you can first try to do some limited model building to the first solution and then use the refined model as template to search. Best wishes.
On Mon, Aug 17, 2009 at 11:42 AM, Yuan Cheng <[email protected]> wrote: > 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 > -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: [email protected]
