Hello Ralf and eversone else
Thanks for your email concerning checksums.

Here is what I am seeing

I started with mymodel (model_mon19), ran one round of refinement against newdatadmm2_unique1.mtz in phenix 1.4.3 with command line like the one below .
Using the output pdb , I rebuilt a lot and renamed pdb to model-fri24.pdb , Now when I try refine using the same input mtz ..phenix complains about rfree checksum mismatch again.

I am assuming that phenix does use the rfree from the mtz file (newdatadmm2_unique1.mtz) and the checksum for the rfree entered in the pdb should have come during round 1 from newdatadmm2_unique1.mtz , so I am a little concerned that it complains.

The command lines I am using are given below: I only change the model , the ncs definition file and the directory in which the refinement is run.
between runs.

Hari

phenix.refine newdatadmm2_unique1.mtz model-fri24.pdb simulated_annealing=true simple_ncs_from_pdb.ncs refinement.main.ncs=true refinement.input.xray_data.r_free_flags.generate=False --overwrite ordered_solvent=true main.number_of_macro_cycles=10 strategy=rigid_body+group_adp+individual_sites refinement.ncs.excessive_distance_limit=None refinement.input.experimental_phases.labels=newdatadmm2_unique1.mtz:HLAC,HLBC,HLCC,HLDC>phenix_fri24.log

Command that wrote the checksum is same as above with model replaced with a model that represented my initial build , untouched by phenix.

On Tue, Apr 21, 2009 at 8:38 PM, Ralf W. Grosse-Kunstleve <rwgk@cci.lbl.gov> wrote:

> Most other things weere the same including the resolution cutoff used and
> the input mtz.
> But phenix tells me that the md5checksums dont match.

Sorry, that's unexpected. The cutoff doesn't matter. The checksum is
computed on the input data, before the cutoff is applied.
The checksum is just a safety guard to avoid accidents. If you are
sure the test set has not changed, simply remove the remark with
the checksum from the pdb file.
Let me know if the problem happens again and I'll take a closer look.
In that case I will need all the input files and the sequence of
commands to reproduce the problem (including the command that wrote
the pdb file with the checksum).

Ralf
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