[phenixbb] Can we untoggle molecular weight mean deviation check on ensembles in autoMR?

James Thompson Thompson.James at mayo.edu
Thu Sep 2 12:09:39 PDT 2010

A postdoc in my lab with many more files inside his Phenix build directory just showed me that the Mwt mean deviation check on input ensembles is hard-coded in Phaser.  A seemingly arbitrary value of 20% is set within the file emsembles.cc.  So, the answer to my previous question is presently NO.  We users cannot untoggle or alter this mean deviation value without some recompile of Phaser.  I will play with my Sculpt'ed output from the Mustang server to reduce the Mwt deviations within the ensemble of coordinates that I want to feed to Phaser-MP to get by.

James R. Thompson <thompson.james at mayo.edu>

> Can folks untoggle the molecular weight mean deviation check in
> phenix.autoMR on the ensembles input?
> I want to use an ensemble of coordinates generated by the Mustangs
> server from a SSM alignment.  Therefore, by design the 10 PDBs input to
> phenix.autoMR vary greatly in molecular weight from their mean value,
> but the whole is likely an excellent probe for molecular replacement.
> However, I am stymied by phenix.autoMR:
> -------------------------------------------------------------------------------------
> FATAL RUNTIME ERROR: Molecular weight of
> /home/jrt04/Desktop/GB1STAS/MUSTANGServer_10_1.6_0_sculpt-coot-0.pdb
> (6610.56) deviates more than 20% from the mean (3977.08). This pdb file
> may contain domains or water not present in the other files. 
> -------------------------------------------------------------------------------------
> I understand why this check might be of utility to the unobservant.  How
> can I disable this test?
> Many thanks,
> Jim
> -- 
> James R. Thompson <thompson.james at mayo.edu>

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