[phenixbb] RSRZ in Phenix? - clarification

[Keller, Jacob]

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