[phenixbb] FOM in table 1

[Nathaniel Echols]

On Mon, Apr 30, 2012 at 10:17 AM, Johan Hattne <jhattne at lbl.gov> wrote:
>
> 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