[phenixbb] on phenix.cut_out_density

Terwilliger, Thomas Charles terwilliger at lanl.gov
Thu Feb 26 07:29:45 PST 2015

Hi Smith,

No, the output of cut_out_density is FWT PHWT and is not interpretable by phenix.refine which requires F,SIGMA.

You may find it easier to use phenix.real_space_refine for this purpose!

If you really want to refine with phenix.refine (make sure you understand all the implications of doing this!)  you can extract FWT and call it FP and add SIGFP=1 with:

phenix.resolve --giant<<EOD
hklin FWT.mtz
labin FP=FWT
mask_cycles 1
minor_cycles 0
solvent_content 0.5
database 5

and copy resolve.mtz to FWT_as_data.mtz, where FP, SIGFP are useable for phenix.refine (but are not "data").

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Smith Lee [smith_lee123 at yahoo.com]
Sent: Thursday, February 26, 2015 6:32 AM
To: PHENIX user mailing list
Subject: [phenixbb] on phenix.cut_out_density

Dear All,

Can the mtz file produced by phenix.cut_out_density be used by Phenix refine for refinement?

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