[phenixbb] AutoMr

Tom Terwilliger terwilliger at lanl.gov
Sat May 9 12:02:17 PDT 2009

Hi Zhongli,

Here are some ideas for you:

If the LLG is negative, it may mean that the RMSD/sequence identity is  
not set quite right. Alternatively the number of copies could be off.

What resolution is your data? Check the R-factor of the MR model  
before and after a quick refinement.  Are they somewhat reasonable  
(i.e., <48% starting, <43% after a little refinement)?  Lower numbers  
than this would indicate that the model is pretty good.

You can run autobuild with your target sequence and MR.1.pdb and it  
will edit the model for you if it can...

If you have 2 different models that fit the data...check to see if  
they really are the same model.  Easiest way:

	phenix.get_cc_mtz_mtz   2FOFC_model_1.mtz   2FOFC_model_2.mtz

will see if there is a simple translation/space-group symmetry  
relationship that will make these 2 maps (and the models they go with)  

All the best,
Tom T

On May 9, 2009, at 11:00 AM, Zhongli Cui wrote:

> 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
> Ph.D
> 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_______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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