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 exceptions of course).

If you only have an existing structure for, say, half of what's in your asymmetric unit, SAD phases will be less biased than model phases from molecular replacement, even though both may be noisy. 



~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Phoebe A. Rice

Dept. of Biochem & Mol. Biol. and

  Committee on Microbiology

https://voices.uchicago.edu/phoebericelab/

 

 



On 12/5/18, 9:14 PM, "CCP4 bulletin board on behalf of James Holton" <[log in to unmask] on behalf of [log in to unmask]> wrote:



    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 heavy atom (more signal) or by doing a lot of averaging (less 

    noise). You will probably need more than one crystal.

    

    SAD, on the other hand, can never give you very good phases because the 

    phase probability distributions are all bimodal. The technology that 

    makes SAD practical is solvent flattening, but as soon as you start 

    doing things like solvent flattening you are already imposing a model, 

    and every model comes with some amount of bias.  How important that bias 

    is depends on the question you are trying to answer.

    

    MIR, like MAD, can get arbitrarily accurate phases, but this and every 

    other technique requires a high degree of isomorphism.

    

    In practice, essentially all experimental phasing attempts are really 

    trying to get you just over that ever-elusive tipping point of phase 

    quality where solvent flattening and model building can take you the 

    rest of the way.  So, in the end what you have are model phases, just 

    like if you had done MR.  It's sad really how fleeting the involvement 

    of experimental phases are in essentially all MAD/SAD structure 

    determinations.  Pun intended.

    

    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, but true.

    

    -James Holton

    MAD Scientist

    

    On 12/5/2018 12:07 AM, 香川 亘 wrote:

    > 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 whether my understanding is correct or not.  If there any good examples or literatures on this issue I would be grateful to know about it.

    >

    > I thank you in advance.

    >

    > Wataru Kagawa

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