Hello Ralf and eversone else<br>Thanks for your email concerning checksums.<br><br>Here is what I am seeing<br><br>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 .<br>
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. <br><br>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. <br>
<br>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.<br>between runs.<br><br>Hari<br><br>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<br>
<div class="gmail_quote"><br>Command that wrote the checksum is same as above with model replaced with a model that represented my initial build , untouched by phenix.<br><br><br>On Tue, Apr 21, 2009 at 8:38 PM, Ralf W. Grosse-Kunstleve <span dir="ltr"><<a href="mailto:rwgk@cci.lbl.gov">rwgk@cci.lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">> Most other things weere the same including the resolution cutoff used and<br>
> the input mtz.<br>
> But phenix tells me that the md5checksums dont match.<br>
<br>
</div>Sorry, that's unexpected. The cutoff doesn't matter. The checksum is<br>
computed on the input data, before the cutoff is applied.<br>
The checksum is just a safety guard to avoid accidents. If you are<br>
sure the test set has not changed, simply remove the remark with<br>
the checksum from the pdb file.<br>
Let me know if the problem happens again and I'll take a closer look.<br>
In that case I will need all the input files and the sequence of<br>
commands to reproduce the problem (including the command that wrote<br>
the pdb file with the checksum).<br>
<br>
Ralf<br>
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