Hi Miles-- Could you please send me the mtz, sca, and pdb files and the .eff file that was written by the GUI? FYI, phenix.refine_gui and phenix.refine should function identically, but until I try running it both ways I can't tell whether the problem is in the GUI or the command-line version. There have been changes to phenix.refine since 1.3-final but these are independent of the GUI. Also, could you check the space group/unit cell information extracted from the files and confirm that these are correct? (This should also be the same as using the command-line version, but it's the only thing I can think of that might cause this problem.) thanks, Nat On Jan 12, 2009, at 12:19 PM, Miles Pufall wrote:

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:

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From: Miles Pufall Date: January 12, 2009 12:16:06 PM PST To: [email protected] 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

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