Here's one - FOM > 0.5 after shelxe, SAD phases, not traceable
Lots of weak data, as truncate shows . . .
Analysis of mean intensity by parity for reflection classes
For each class, Mn(I/sig(I)) is given for even and odd parity with respect to
the condition,
eg group 1: h even & odd; group 7 h+k+l even & odd; group 8 h+k=2n & h+l=2n &
k+l=2n or not
1 2 3 4 5 6
7 8
h k l h+k h+l k+l
h+k+l h+k,h+l,k+l
Totals: 22.0 22.9 21.9 23.0 39.4 5.3 39.4 5.3 21.9 23.0 22.0 22.9
22.4 0.0 37.9 17.0
The stats from shelxe for an incorrect solution
Mean weight and estimated mapCC as a function of resolution
d inf - 2.43 - 1.93 - 1.68 - 1.52 - 1.41 - 1.33 - 1.26 - 1.21 - 1.15 - 1.06
<wt> 0.581 0.625 0.614 0.610 0.603 0.594 0.600 0.583 0.574 0.547
<mapCC> 0.988 0.981 0.979 0.980 0.978 0.979 0.978 0.975 0.969 0.955
N 4117 4037 4172 4272 4177 3923 4338 3632 4456 3638
Pseudo-free CC = 75.58 %
and the other hand
Mean weight and estimated mapCC as a function of resolution
d inf - 2.43 - 1.93 - 1.68 - 1.52 - 1.41 - 1.33 - 1.26 - 1.21 - 1.15 - 1.06
<wt> 0.589 0.635 0.617 0.622 0.623 0.621 0.625 0.610 0.602 0.579
<mapCC> 0.987 0.982 0.981 0.982 0.980 0.983 0.982 0.978 0.976 0.968
N 4117 4037 4172 4272 4177 3923 4338 3632 4456 3638
Pseudo-free CC = 78.72 %
and the correct solution, which was traceable
Mean weight and estimated mapCC as a function of resolution
d inf - 2.43 - 1.93 - 1.68 - 1.52 - 1.41 - 1.33 - 1.26 - 1.21 - 1.15 - 1.06
<wt> 0.571 0.623 0.612 0.621 0.623 0.618 0.623 0.608 0.615 0.605
<mapCC> 0.987 0.984 0.983 0.984 0.982 0.984 0.983 0.980 0.980 0.975
N 4117 4037 4172 4272 4177 3923 4338 3632 4456 3638
Pseudo-free CC = 85.42 %
Pete
-----Original Message-----
From: CCP4 bulletin board on behalf of James Holton
Sent: Sat 9/8/2007 8:57 AM
To: [email protected]
Subject: Re: [ccp4bb] just how bad can phases be and still help
In my experience, the "threshold of interpretability" for electron
density maps is when the FOM is ~0.5 or higher. I am basing this on
anecdotal responses to this movie:
http://bl831.als.lbl.gov/~jamesh/movies/index.html#phase
In this case, the displayed value for FOM is exact. Depending on how
you are estimating FOM, your mileage may vary.
As noted on another thread, different programs do indeed report
different values for the same statistic. The reason why different
programs give different FOMs is because the definition of FOM is the
cosine of the difference between the reported phase (output by the
program) and the "true" phase. Since you obviously don't know the
"true" phase, this is a hard number to figure out. Every phasing
technique has a different method of estimating the FOM, but all of them
are just that: estimates. In fact, it is somewhat preposterous to try
to compute the deviation from some unknown "correct" value, which is why
we have so many other phase quality statistics like phasing power, lack
of closure, RCullis etc. These are at least well-defined for a given
data set, but unfortunately don't have much more than an empirical
correlation to the number you really want to know: FOM.
Map interpretability depends on the "true" FOM, but unfortunately, all
we have to work with is the FOMs we can estimate. There are sometimes
practical reasons for underestimating the FOM (see the mlphare manual),
and a solvent-flattening job that is allowed to run for far too many
cycles will get phase bias and overestimate the FOM. I can say that
in controlled tests I have done, the FOM reported by dm (if you have a
modern version and let it decide when to stop cycling) tends to be
fairly accurate. Yes, it does depend on resolution, but if you have
high-res data with very low FOM, then you basically don't have any
high-res data in an FOM-weighted map. I tend to predict map
interpretability by asking the question "to what resolution limit is the
average FOM > 0.5?" If that is 10A, then I generally don't bother
looking at the map.
Perhaps the best way to settle this is to put it out to a challenge:
does anybody have a map calculated with an average FOM(fromsomeprogram)
< 0.5 that they were able to trace? Does anyone have a map calculated
with FOM(fromsomeprogram) > 0.5 that was total garbage?
-James Holton
MAD Scientist
Bryan W. Lepore wrote:
> general question - perhaps the fundamental question -
>
> for anyone who had "weak/poor/bad" phases from some source, that were
> later actually used to solve a structure when combined w/ another
> source - HOW bad were the worst phases on their own, in terms of
> resolution, FOM, CC, e-density, (any other numbers)? what was MOST
> important in knowing the phases would help (presumably e-dens.).
>
> i.e, was it only when relatively "better" phases gave any
> interpretable density that it was known that the "bad" phases would help?
>
> -bryan
