[phenixbb] Experimental Data Question

Nathaniel Echols nechols at lbl.gov
Fri Jul 15 13:37:28 PDT 2011

On Fri, Jul 15, 2011 at 1:27 PM, Yuri <yuri.pompeu at ufl.edu> wrote:
> I collected data on a new crystal, indexed, scaled (2.75 A), ran molecular
> replacement (40% homologue) and found a solution.
> I did some building got a new model, did an initial refinement (using my
> .sca file, not data.mtz from mol rep).
> I then ran phase_and_build with density modification. The new maps look a
> lot better and I am able to see some residues I was not able to place
> before.
> I did some more building and I am ready to refine. What should I use as
> experimental data?
>  phase and_build gave me a .mtz file with amplitudes (no I) and
> "experimental phase" coeeficients (HLAM. HLBM,...)

You should use the file ending in _data.mtz output by phenix.refine
after the initial refinement - this contains your amplitudes and the
R-free flags that phenix.refine generated, and it's essential that you
continue to use these.  What did you use as input for phase_and_build?
 It will create its own R-free flags if none are found in the input
file, which in this case would be bad.

(You definitely should not use the Hendrickson-Lattman coefficients
output by phase_and_build - only experimental phases from AutoSol,
etc.  Unfortunately our software is not [yet] smart enough to tell the
difference, since they're all the same in the MTZ files.)


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