By popular demand we (by which I mean Airlie McCoy) have put in a new option to bypass the molecular weight deviation check. So in a script-driven Phaser run you could add a command like ENSEMBLE ensemble1 DISABLE CHECK ON. However, there isn't yet an option to disable this in the GUI. That might turn out to be a temporary solution. The reason for the deviation check is that an ensemble is assumed to represent a set of alternative models for the same component, and if the individual models cover significantly different parts of the structure, that assumption is violated. Initially we allowed 10% deviation then increased that to 20% -- it's a relatively arbitrary number chosen conservatively to be on the small side but nonetheless sufficiently forgiving for the test cases we had at hand. When we get a chance, we'll have a look at the consequences of violating the assumption that the alternative models cover the same part of the structure and do what seems appropriate based on that -- set an evidence-based threshold, do away with it altogether or come up with an improved way of dealing with ensembles. Regards, Randy Read On Sep 2 2010, James Thompson wrote:

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

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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