[phenixbb] RSRZ in Phenix? - clarification
Keller, Jacob
kellerj at janelia.hhmi.org
Sun Dec 27 20:52:54 PST 2015
Pardon my dogged personal interest here, but why are these calculations not done with twinned data in Phenix, since those maps are made anyway?
JPK
-----Original Message-----
From: Pavel Afonine [mailto:pafonine at lbl.gov]
Sent: Sunday, December 27, 2015 11:15 PM
To: Randy Read
Cc: Keller, Jacob; phenixbb at phenix-online.org
Subject: Re: [phenixbb] RSRZ in Phenix? - clarification
Reading my own email again after sending it to you (yes, I do have that odd habit!) I realized that this sentence is or may be confusing as written:
"""
In case of a group that contains several atoms, we will be looking at average of 2mFo-DFc and mFo-DFc map values at atom centers, and CC is computed as above using map values inside atom spheres.
"""
What I really meant here is average of 2mFo-DFc map values at atom centers, and average of mFo-DFc map values at atom centers, (two values for two kinds of maps), and NOT "average of 2mFo-DFc and mFo-DFc map values at atom centers" as it in original email.
I'm sorry for the confusion!
Pavel
On 12/27/15 12:40, Pavel Afonine wrote:
> Hi Randy,
>
>> The argument for RSRZ last time we had the PDB X-ray validation task
>> force was that it's meant to be independent of resolution and residue
>> type, i.e. if you're trying to judge how well someone did in fitting
>> a structure, you expect a much better CC for a Trp in a 1.8A
>> resolution structure than you do for a Lys in a 2.8A resolution
>> structure. The RSRZ score compares the RSR for the residue type at
>> its resolution with other residues of the same type at similar
>> resolution. (We used RSR because Gerard K had generated the
>> statistics for that one and hadn't done the same for RSCC, which may
>> or may not have had advantages.)
>>
>> However, it definitely has its problems. For example, the RSRZ for a
>> side chain in a 6A structure makes no sense whatsoever because, in
>> order to get enough representatives of each residue type to generate
>> statistics, you have to include all the structures from something
>> like 3.5 to 8A resolution! So we're looking for better alternatives
>> this time around in the VTF.
>
> thanks a lot for explanation, it is very helpful!
>
>> Suggestions with evidence are welcome!
>
> Assuming we are talking about local model-to-map fit so that we focus
> on a goodness of fit of an atom or a few atoms (such as residue or
> ligand), I still think that a triplet of numbers {2mFo-DFc map value,
> mFo-DFc map value, CC} calculated per group of atoms in question is
> something to consider.
>
> In case of a group that contains just one atom, we will be looking at
> 2mFo-DFc and mFo-DFc map values at atom center, and CC between the map
> in question and Fmodel map, calculated in a sphere R around the atom,
> with Fmodel map being the Fourier transform of the total model
> structure factor Fmodel = ktotal * (Fcalc_atoms + Fbulk_solvent).
>
> In case of a group that contains several atoms, we will be looking at
> average of 2mFo-DFc and mFo-DFc map values at atom centers, and CC is
> computed as above using map values inside atom spheres.
>
> Why I think {2mFo-DFc map value, mFo-DFc map value, CC} is good?
>
> 1. If 2mFo-DFc map is scaled by standard deviation we kind of know, as
> a rule of thumb, what is good value and what is poor one. With
> cctbx/Phenix tools it is a day long exercise collect any desired
> statistics for 2mFo-DFc map values over entire PDB: we can bin it by
> resolution, various types of completeness, by residue/atom types, etc
> etc you name it. Thus we could turn "a rule of thumb" above into
> sometime more scientific-like.
>
> 2. Even if 2mFo-DFc map value is good, an atom may still be slightly
> misplaced or its parameters (xyz, q, B) may not be well refined. This
> will be immediately highlighted by mFo-DFc map value. In fact, it is a
> good target in a sense that we don't even need a "rule of thumb"
> values for it: the flatter mFo-DFc, the better.
>
> 3. 2mFo-DFc and mFo-DFc maps as suggested to be used above are still
> insufficient because the map shape is not taken into account. One may
> envision a situation of incorrect atoms filling the map such that
> 2mFo-DFc is strong enough and mFo-DFc is rather flat but the shape of
> the construct does not resemble the actual map well. This is what the
> map CC will help us with, as it is scale-insensitive but shape
> sensitive! Actually, CCr from
>
> http://journals.iucr.org/d/issues/2014/10/00/kw5094/kw5094.pdf
> Acta Cryst. (2014). D70, 2593-2606
>
> would be even much better than regular CC.
>
> 4. An advantage of using the above mentioned metrics (all together!)
> is that they are old well established quality measures that majority
> of crystallographers have more or less clear idea about, both the
> meaning and what to expect as a numerical value. No need to re-invent
> the wheel! (except from gathering some statistics on expected map
> values).
>
> All the best,
> Pavel
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