[cctbxbb] Re: chiral validation

Hi On Mon, Nov 4, 2024, 4:49 PM Christopher Williams < [email protected]> wrote:

Hi James,

The chiral validation in Phenix is looking at chiral volumes. I believe these are calculated using dihedrals. The chiral volume value is signed, and will change sign if the handedness of the chiral center switches.

One of the basic text outputs of phenix.chiral_validation looks like this: atoms ideal model delta sigma residual deviation A 101 THR CB A 101 THR CA A 101 THR OG1 A 101 THR CG2 2.55 1.70 0.85 2.00e-01 1.82e+01 4.3*sigma

This lists the 4 atoms involved in calculating the chiral volume, starting with the chiral center in question (CB here). Ideal is the target value, found in the .cif's in geostd Model is the measured value for the chiral center in question Delta is the difference between ideal and model Sigma is is esd value associated with the target, also found in the .cif Deviation is the number of sigmas away from the Ideal that the Model is

If you use the json=True flag, you can get some additional output that attempts to categorize chiral volume outliers, in the "outlier_type" field. This additional output also appears on MolProbity and in the Phenix GUI.

There are 3 categories of chiral volume outlier: -"Chiral handedness swaps" are true chiral switches like DAL for ALA. These have a large abs(Deviation) (>10*sigma)

-"Tetrahedral geometry outliers" are squashed or flattened chiral centers. Usually the result of geometry distortions or strain, much like bond length or bond angle outliers. I believe these have a abs(Deviation) between 4 and 10. Their geometry is distorted enough that MolProbity is hesitent to make anyclaim about what the intended handedness was.

-"Pseudochiral naming errors" are for atom centers that appear chiral due to chemical naming conventions, but which are not chemically chiral. Iron-sulfur clusters are vulnerable to this sort of mis-naming. As are the P of DNA/RNA backbone (if OP1 and OP2 names are swapped), the CB of VAL (CG1/CG2) and the CG of LEU (CD1/CD2). These represent a bookkeeping error (that should be fixed) rather than a modeling error.

A explanation with KiNG visuals here: http://molprobity.biochem.duke.edu/help/validation_options/validation_option...

Hope that helps. And thank you for noticing that the help text is incorrect.

Regards, -Christopher Williams ---Richardson Lab, Duke University

On Sun, Nov 3, 2024 at 11:18 AM James Holton wrote:

...

Can anyone tell me the units of the numbers being displayed by phenix.chiral_validation? The --help documentation doesn't mention anything about chirality. Seems to be a copy of the documentation for omegalyze?

Just thought that might be of interest, and I also want to know what the numbers mean.

Cheers,

-James

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