On Tue, Feb 26, 2013 at 10:32 AM, Matthew Franklin
(Disclaimer: I usually use phaser in ccp4, and I don't have the latest version. Not everything I say may be applicable.)
Airlie and I put a fair amount of work into making sure that the defaults in the CCP4 version and the Phenix version should be the same, at least to whatever extent they're using [approximately] the same source revision. (Our nightly builds - official releases included - are always using the very latest code. Not sure what CCP4 does.)
I'm not sure how to make Phaser do this in Phenix, but I see in the "Phaser-MR" window that there is an "Other Settings" button; in the window this pops up, you can try selecting "allow" for the packing function then "20" for the cutoff. This should work...
I have to admit, this is very poorly labeled right now. I think your advice is correct, but I have added much better captions and help text for the packing options (in the next build, of course). -Nat