[phenixbb] AutoMr

Zhongli Cui czl at njau.edu.cn
Sat May 9 10:00:07 PDT 2009

Dear all,
I am using phenix automr to solve my structure. I have 2 search models with identiy of 44% and 31% respectively aligned by ClustalW. I used thiese two pdbs as search models directly in phenix, it gave a llg of about -60 and Tfz of 7. The refined structure fit the map quite well. But I wonder if the solution is OK for the negative LLG. So what should I do next? How should I prepare the search model? Shall I edit the seach models such as remove some loops or surface side chains? If I the a search model prepared by Chainsaw was used, then what is identity I have to tell phenix?
Another question, I built 2 models of the same protein and of the same x-ray diffraction data with phaser in CCP4 and Phenix. In my mind, these models should be the same. But in fact they differ from each other significantly in orientation. Is there something wrong with my calculation?

Cui Zhongli

Dept. of Microbiology
College of Life Sciences
Nanjing Agricultural University
1 Weigang, 
Nanjing, 210095
Jiangsu Province
P.R. China.
Mail: czl at njau.edu.cn
Tel: 86-25-84396753
Mob: (0)13951080529
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