Hi,
> Any time you do a thought experiment you make a fake-data data set, the
> "true" phases and "true" amplitudes become the ones you put into the
> simulation process. This is by definition. Is there potential for
> circular reasoning? Of course! But you can do controls:
>
this is so much
What may be counter-intuitive when looked at in one way may be
perfectly expected from another point of view. I look at these maps as
the result of a single cycle of steepest descent refinement where the
parameters are the density values of the map sampled on the grid. If
you start with a map
Sorry for the confusion, I was going for brevity.
Any time you do a thought experiment you make a fake-data data set, the
"true" phases and "true" amplitudes become the ones you put into the
simulation process. This is by definition. Is there potential for
circular reasoning? Of course! Bu
A point I like to make to new trainees trying to solve structures:
Model phases from a good model are pretty good, but from a practical viewpoint,
if your initial model for molecular replacement is that good, the resulting
structure will probably not tell you much you didn't already know (with
e
JISCMAIL.AC.UK] Im Auftrag von Keller,
Jacob
Gesendet: Donnerstag, 6. Dezember 2018 04:37
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Experimental phasing vs molecular replacement
>>That said, model phases are not so bad. In fact, in all my experiments with
>>fake data th
>>That said, model phases are not so bad. In fact, in all my experiments with
>>fake data the model-phased 2mFo-DFc map always has the best correlation to
>>the "true" map. If you substitute the "true" phases and use the 2mFo-DFc
>>coefficients you actually make things worse. Counter-intuitive
It is true that MAD phasing can give you hyper-accurate phases. This is
because you are measuring the heavy atom signal in both directions on
the Harker diagram, allowing the phase to be solved analytically. The
phasing signal is noisy, of course, but you can fix that either with a
bigger heav
Hello,
I think what you are alluding to is model bias in (macromolecular)
crystallography. What you should consult are the publications associated
with this topic, and those on the map coefficients used to compute
electron density maps (e.g. SIGMAA weighting), OMIT maps, current
refinement te
Dear all,
It is my understanding that experimental phasing (e.g. Se-SAD), in principle,
yields better electron density maps than molecular replacement for protein
regions with weak electron densities (partially disordered or flexible). I
would appreciate if someone could provide comments on wh
