[phenixbb] Fwd: Refinement using new Phenix causes electron density/model mismatch

Miles Pufall mpufall at cmp.ucsf.edu
Mon Jan 12 12:19:36 PST 2009


The bb bounced my email back because the enclosures were too big - let  
me know if you'd like them.

Thanks -

Miles


Begin forwarded message:

> From: Miles Pufall <mpufall at cmp.ucsf.edu>
> Date: January 12, 2009 12:16:06 PM PST
> To: phenixbb at phenix-online.org
> Subject: Refinement using new Phenix causes electron density/model  
> mismatch
>
> Hi Guys -
>
> I am having a very puzzling problem using the new Phenix (1.4-3).  I  
> have about 20 structures that I am preparing to deposit with an  
> accepted manuscript, and decided to do a final refine using the  
> phenix.refine_gui not only to see if I got better numbers, but to  
> use the integrated validation tools, which I love.  Unfortunately,  
> often, but not always, when I refine the pdb against the  
> *_refine_data.mtz the statistics are a bit worse, and when I open  
> the resulting *.map_coeffs.mtz in Coot it appears to be shifted with  
> tons of negative electron density.  Needless to say, this is making  
> my nervous, so I've tried a few things:
>
> 1)  Tried refining the same .pdb and .mtz files in Refmac - I seem  
> to get the same shifting.
> 2)  Try using the old .def file left over from the final run (just  
> to make sure I didn't screw up some setting) - and I get the same  
> shifting.
> 3)  Try refining against the original .sca file - and I get the same  
> shifting.
> 4)  Try molecular replacement of the refined .pdb against the  
> original .sca file - and sometimes, but not always, get a shift.
>
> I am nervous and concerned - can you help me figure out what  
> happened?  I am enclosing an example -
>
> refine_001.pdb = pdb I refined in new phenix
> refine_001map_coeffs.mtz = mtz output from new phenix refinement  
> (lots of red)
> oste44a_output.sca = original scale file from HKL2000
> MR.1_refine_data.mtz = data from which I am refining
> sgk_ost_temp_H_refine_004.pdb
>
> Thanks -
>
> Miles
>
> Miles Pufall
> Postdoctoral Scholar
> Yamamoto Lab
> UC San Francisco
> Cellular and Molecular Pharmacology
> Mail Stop 2280
> 600 16th Street, Genentech Hall S-574
> San Francisco, California 94158-2517
> (415)476-4480
>
>

Miles Pufall
Postdoctoral Scholar
Yamamoto Lab
UC San Francisco
Cellular and Molecular Pharmacology
Mail Stop 2280
600 16th Street, Genentech Hall S-574
San Francisco, California 94158-2517
(415)476-4480


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090112/91ab8e8e/attachment-0003.htm>


More information about the phenixbb mailing list