[phenixbb] rfree checksums version 1.3 and 1.4

hari jayaram harijay at gmail.com
Fri Apr 24 07:55:37 PDT 2009

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.


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

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 at 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
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