[phenixbb] autosol ?

Tom Terwilliger terwilliger at lanl.gov
Thu Sep 16 09:41:07 PDT 2010

Hi Ram,

I don't have a good answer to your questions; perhaps others will.  Here are some thoughts:

> I have collected Cu anomalous peak data (low resolution with high redundancy). Also I do have model and tried to do difference fourrier using 
> Phenix.automr and phenix.autosol.
> Phenix found three sites with significant peak height 10, 9 , 8, rest of them 4.0. But all the three sites are close to methionine ?

I think you placed your model with phenix.automr (or below with phaser) and then used autosol with input_partpdb_file=your_model.pdb to identify sites, is that right?  Now the sites you got with peak heights of 10,9,8 sigma sound reasonably high, yes.  Are they right where SD of methionine is located, or some distance away such as 4-5 A?  Where do you expect the Cu to be located?
> Also I do have some unusual, I tried molecular replacement with phaser and phenix.automr. Phaser found the dimer with correlation
> TZ 9.0 and 14, but phenix.automr , failed to find the model. It is very low resolution data. 

If you are using phenix for phaser and phenix.automr, then the difference is probably just the parameters used in your phaser run vs your automr run; perhaps the allowed number of clashes is different or the RMSD input is different?  

All the best,
Tom T
> Thanks
> ram
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
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