Author(s)

• holton_geometry_validation: James Holton (Python coding by Tom Terwilliger)

Purpose

Summarize geometric quality of a model

How holton_geometry_validation works:

This tool summarizes the geometric quality of a model by calculating pseudo-energies for every aspect of a model (each bond length, angle, rotamer, Ramachandran value, etc). For each metric (such as angles), the mean value and worst value of the pseudo-energy are calculated, and the probabilities of this mean and this worst value not occurring by chance are estimated. To reduce the dominance of very poor values, energy values over 10 are filtered by reducing them toward 10 with a logarithmic function.

The weighted energy for each metric is sum of the mean energy and the filtered worst energy for that metric, each weighted by their probabilities of not occurring by chance.

The overall energy is the sum of weighted energies for all metrics. The metrics used are:

CBetadev: Deviation of CB position from ideal (A)
Clash:    Clash of non-bonded atoms (A)
Omega:    Peptide omega angle deviation (degrees)
Rama:     Ramachandran outlier probability
Rota:     Rotamer outlier probability
Angle:    Angle deviation (degrees)
Bond:     Bond length deviation (A)
Chir:     Chirality deviation (A**3)
Torsion:  Torsion angle deviation (degrees)
Full-nonbond: Non-bonded deviations, including all instances
Nonbond:  Non-bonded deviations (using Lennard-Jones potential,
          excluding bonds that are plausible and have low energies)
Plane:    Planarity deviations (A)

Estimate of expected energy for ideal structure

This tool estimates the expected energy for a structure that has all bonds, angles, etc, distributed as normal distributions with the sigmas used in the geometry validation step above. That is, if the structure had a normal distribution of errors, it would have about this energy. The energy is estimated by sampling from a normal distribution when calculating the energy terms instead of taking the actual deviations. The sampling process is carried out many times (20) and the averages are reported.

Estimate of ratio of deviations to sigmas

The tool estimates the overall ratio of deviations to sigmas in three steps

First it lists all the values deviation/sigma for all the metrics. If the deviations were drawn from random Gaussian distributions with standard deviations of their corresponding sigmas, these values of deviation/sigma would be normally distributed with a standard deviation of one.

Then the 99.7th percentile of values of deviation/sigma is noted. For a Gaussian distribution, this percentile corresponds to 3 standard deviations. The estimated ratio of deviations/sigma overall is then 1/3 of this 99.7th percentile value, or 1 standard deviation of the ratios of deviation to sigma.

Uses

You can use holton_geometry_validation to compare models for the same structure and identify which has fewer overall geometric problems.

You can use the expected energy to see if your structure has errors that are about what is expected based on ideal model geometry and uncertainties.

You can use the estimate of ratio of deviations to sigmas to further examine whether the deviations from ideality in your structure are about what is expected based on the expected variation in geometric values.

Examples

Standard run of holton_geometry_validation:

Running holton_geometry_validation is easy. From the command-line you can type:

phenix.holton_geometry_validation 1ss8_A.pdb

where 1ss8_A.pdb is the model you would like to evaluate.

Possible Problems

If your structure has hydrogen positions that do not match those expected by Phenix, you can ignore them in all metrics except non-bonded interactions with ignore_h_except_in_nonbond=True. Alternatively you can redo their positions with keep_hydrogens=False.

If you want to ignore just hydrogen positions in Arginine residues, you can specify ignore_arg_h_nonbond=True.

If you want to exclude hydrogen nonbond contacts involving waters, use ignore_water_h_bonds, and if you want to exclude all bonds involving hydrogen, ignore_bond_lengths_with_h=True

Literature

The method is described at https://bl831.als.lbl.gov/~jamesh/challenge/twoconf/#score

Additional information

List of all available keywords

• model = None input PDB file
• get_individual_residue_scores = None Calculate individual residue scores in addition to overall score
• round_numbers = True Round numbers before calculation
• worst_clash_is_one_plus_n_times_worst_clash = True Scale worst clash score by (1 + n) where n is total clashes
• clash_energy_add_n = True Add number of clashes to clash energy score
• minimum_nonbond_score_to_be_worst = -0.1 Only include worst nonbond score if it is at least this value
• minimum_nonbond_score_to_be_included_in_average = 0 Only include nonbond score in average if it is at least this value
• include_full_nonbond_score = True If set, add additional scoring term in which all nonbond values (even those less than the minimums) are included
• keep_hydrogens = True If set, keep input hydrogens, but add any necessary riding H.
• ignore_cis_peptides = False If set, ignore cis peptides. Otherwise (if False), penalize them.
• ignore_h_except_in_nonbond = True If set, ignore H atoms except in nonbond term
• ignore_arg_h_nonbond = True If set, ignore H atoms in Arginine
• ignore_bond_lengths_with_h = False If set, ignore bond lengths involving H atoms
• ignore_water_h_bonds = False If set, ignore nonbonded contacts with water hydrogens
• rotalyze_ramalyze_max_energy = 99 Maximum value of energy for a bad rotamer or phi-psi combination
• overall_max_energy = None Maximum value of energy
• omega_angle_sigma = 4 Sigma for omega angle
• cbetadev_sigma = 0.05 Sigma for CB position
• clashscore_ideal_dist = 3 Ideal distance in Lennard-Jones potential for clashscore result
• lj_dist_that_yields_zero = 6 Distance at which modified Lennard-Jones potential crosses zero
• softPnna_params
  • y0 = 1 Parameter y0 for softPnna calculation
  • a2 = -0.0192266 Parameter a2 for softPnna calculation
  • a1 = 0.751694 Parameter a1 for softPnna calculation
  • a0 = 1.12482 Parameter a0 for softPnna calculation
  • mx = 0.21805 Parameter mx for softPnna calculation
  • my = 0.736621 Parameter my for softPnna calculation