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On 10/05/2011 03:42 PM, Peter Canning wrote: > When I run Parrot to do density improvement and NCS averaging, Parrot > works beautifully (final FOM is 0.87) but NCS averaging causes the > average NCS correlation coefficient to drop (from 0.94 to 0.64) and the > average mask volume to increase from 0.31 to 0.7 (minimum volume > increases from 0.05 to 0.07 and maximum volume goes from 1.2 to 2), > which seems a bit high. Not impossible if the NCS is along a special direction. I've rewritten the logfile stats in the latest version to give you a more meaningful and less confusing number. > Unless I have misunderstood something, I thought the NCS correlation > coefficient should increase during averaging and the average mask volume > should decrease. If this is the case, has anyone any idea what I’m doing > wrong? That's true for experimental phasing. When you start from MR, your initial phases contain the NCS implicitly. The structure factor magnitudes in this case have something to say about the differences between the molecules. Again, I think the stats in the new version may be more informative. > Also, at the risk of asking a dumb question, is there a particular way > my Parrot modified file should be input into Refmac to get the best > results? The FOM from my refmac runs never seems to be as good as that > output by Parrot. FOM from density modification is overestimated! From refmac less so! K