On Mon, Apr 30, 2012 at 10:17 AM, Johan Hattne
On 29 Apr 2012, at 23:55, Dialing Pretty wrote:
In some table 1 of the crystallography paper, there is an item called "FOM". Will you please explain the meaning of it? Do we have a server to get it or some other route to get this value?
I'm guessing this is the "figure of merit", defined as the cosine of the phase error. Since the correct phase is generally unknown it's an estimate, which may be calculated during density modification (phase improvement).
It will probably appear somewhat in the phenix.refine log file as well, in one of the tables at the end: stage <pher> fom alpha beta 0 : 55.378 0.4528 0.8776 905662.442 1_bss: 49.163 0.5316 1.2928 650255.977 1_xyz: 46.167 0.5687 1.3802 559471.522 1_adp: 40.720 0.6353 1.4942 483440.556 2_bss: 41.137 0.6303 1.4612 505402.815 2_xyz: 36.144 0.6885 1.5241 412562.858 2_adp: 33.622 0.7173 1.4769 378709.335 3_bss: 33.992 0.7133 1.4808 392255.409 3_xyz: 33.219 0.7213 1.5110 375299.213 3_adp: 32.144 0.7339 1.3212 366007.489 3_bss: 32.351 0.7318 1.3162 372771.223 But like Johan says, it's an estimate, and not a very useful number for evaluating the final model quality - however, the FOM for experiment phasing is a relatively good estimate of the quality of the initial map, and I suspect most papers which include it may be referring to this, not the value for the refined model. If you didn't use experimental phasing for your structure, I wouldn't bother reporting the FOM unless the journal (or a reviewer) requires it. -Nat