[buster-discuss] free R flag questions
Claus Flensburg
claus at globalphasing.com
Fri Sep 24 11:08:31 CEST 2010
Hi Wolfram,
On Wed, Sep 22, 2010 at 08:40:14PM -0600, wtempel wrote:
> Hello.
> Here are some excerpts from stdout of an initial autobuster "refine" run.
> <excpt>
> ################################ Basic checks
> ################################
>
>
> ESC[1mNOTEESC[m : running with the following command line arguments:
> "-p ../201009222206.pdb -m ../output_PHENIX0phs2.mtz
> -autoncs ColumnName_FreeR_flag=Free-Phenix -R 30
> 2.58"
>
> </excpt>
>
> During the first autobuster run, the ccp4 program unique seems to be
> invoked. And I get this warning:
>
> <excpt>
> ESC[1mWARNINGESC[m : had to create a fresh test-set column - usually
> the MTZ file should already contain this!
>
> F/SIGF pairs : FP,SIGFP
>
> ##############################################################################
>
> # refining against FP,SIGFP with: Free-Phenix
> ##############################################################################
> </excpt>
>
> Can I ignore this warning regarding the "fresh test-set column"?
yes, it should be harmless. It can be avoided by doing:
% refine ... ColumnName_FreeR_flag_allowed=" I[ ]* Free-Phenix" ...
> Will that
> new test-set column be used in any way?
no, it shouldn't.
> And related to this, is there some command line switch that allows me to
> specify a non-0.00 value that flags "free" reflections?
well, yes, the following should do that:
% cat >> .autoBUSTER<<EOF
BusterExtraKwds="FREFLG=2"
EOF
% refine ...
to use a value of 3 for the test set reflexions.
Regards,
ClAuS + BDG
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