leonarski_fandClaude Opus 5.5
1f27fba1f3
- ModelValidation reads the model and, where it carries non-given NCS operators (_struct_ncs_oper 'generate' / MTRIX without the given flag), expands them (gemmi expand_ncs, vendored assembly.cpp from GEMMI 0.7.5, MPL-2.0 as the rest of gemmi_gph). Same in the battery's model_check.py and depdata_check.py. An icosahedral-virus entry deposited as 3 of the 45 chains of its ASU was scored against a fifteenth of its atoms: R-free 0.545 -> 0.297. - The indexing the model chooses (AdoptModelFrame) now moves the cell with the indices (reseat_integrated in the main path; CellInBasis in the forecast, twin-file and stills/scale paths). A near-symmetry law (b within 2% of c, beta a degree off 90, a~b in P1) relabelled the reflections only, so the files were written with two axes swapped or beta flipped relative to the indices. Where the law moved the cell, the validation is remade on the moved cell. Measured on 18 open/in-house sets with models: p.hkl and MTZ reflection data bit-identical on all; cell and model R unchanged where the law is exact; the cell now matches the deposited one on the 6 pseudo-merohedral cases (orthorhombic a/c swap, three monoclinic beta flips, a P1 alpha/beta swap), R-free within +-0.001 there. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3
710 lines
35 KiB
Python
710 lines
35 KiB
Python
#!/usr/bin/env python3
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"""model_check.py -- R-factors of the deposited model against Rugnux's merged data.
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An external check for the open arm, run AFTER Rugnux has written its MTZ, so it cannot bias the
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processing (Rugnux is never given the model). For one set it:
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* fetches the entry's mmCIF (and, for the baseline, its structure factors) from RCSB into a
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cache, and reads the published R-work / R-free / d_min from the entry's `_refine`;
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* matches the data to the model's setting: the two lattices are compared through their Niggli
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cells, every change of basis that carries one onto the other is tried (this covers an
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alternative setting, a permuted or centred-vs-primitive description and the merohedral
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indexing ambiguity), and the one whose reindexed data agree best with the model's Fcalc on a
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mid-resolution shell is taken;
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* re-expresses the data in the DEPOSITED space group: expanded to P1 with Rugnux's own group,
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reindexed, reduced to the deposited group's asymmetric unit (an over-call just splits
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equivalents apart, an under-call averages them) and given the DEPOSITED cell;
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* has REFMAC compute R-work / R-free of the model AS DEPOSITED, with its bulk solvent and
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overall anisotropic scaling, at the lower of the two high-resolution limits. This is REFMAC's
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rigid-body mode read at its first cycle, before any shift is applied: rigid body reads no
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restraint dictionaries, so no ligand is stripped, no atom is moved and no cell is imposed on
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the model. Refining is deliberately not done - the data were moved into the model's frame, so
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there is nothing for a rigid body to correct, and at low resolution REFMAC's rigid body can
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walk a correct model away (R 0.30 -> 0.49 over ten cycles on one 5 A set);
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* scores the SAME model with the SAME protocol against the depositor's own structure factors
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and free set, as the baseline for "same method, other data", and - when that free set can be
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carried over - also scores Rugnux's data on the depositor's free reflections. The depositor's
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data go through the same setting choice as Rugnux's (they can be indexed in the other branch
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of a merohedral ambiguity); where only intensities were deposited, amplitudes come from
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ctruncate's French-Wilson;
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* scores an entry that declares twinning (_pdbx_reflns_twin) with REFMAC's twin refinement,
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both data sets alike, and keeps the untwinned numbers beside it;
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* and, as a second protocol (refined_*), refines the same deposited model against each data set
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at its OWN resolution (restrained, same protocol for both) with R-free on a SHARED free set:
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the depositor's free reflections present in both data sets (see refined_shared).
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The first-cycle numbers are taken at d_min_used = max(Rugnux's d_min, the deposited d_min).
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On free sets: the depositor's model was refined against every reflection except THEIR free set,
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so most of Rugnux's free reflections were work reflections to it. `rfree` (Rugnux's own flags)
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therefore reads like a work R. `rfree_depflags` (depositor's flags on Rugnux's data) is the
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number that is comparable with `rfree_depdata` and, loosely, with `rfree_deposited`.
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model_check.py rugnux.mtz 1abc [--workdir DIR] [--cache DIR] [--no-baseline]
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"""
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import argparse
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import itertools
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import json
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import os
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import re
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import subprocess
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import time
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import gemmi
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import numpy as np
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DEFAULT_CACHE = "/data/battery/pdb_cache"
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CCP4_SETUP = os.environ.get("CCP4_SETUP", "/opt/xtal/ccp4-9/bin/ccp4.setup-sh")
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RCSB = "https://files.rcsb.org/download/"
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PDB_ID = re.compile(r"^[0-9][a-z0-9]{3}$")
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MAX_ATOMS = 200000 # REFMAC time grows with atoms x reflections
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CELL_TOL = 0.05 # Niggli cells compared loosely on purpose; the R score decides
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ANGLE_TOL = 3.0
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REFINE_CYCLES = 10 # restrained refinement of the shared-free-set protocol
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# ------------------------------------------------------------------ deposition
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def fetch(url, dest):
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if not os.path.exists(dest) or os.path.getsize(dest) == 0:
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tmp = dest + ".part"
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r = subprocess.run(["curl", "-sfL", "--max-time", "300", "-o", tmp, url])
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if r.returncode != 0 or not os.path.exists(tmp):
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if os.path.exists(tmp):
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os.remove(tmp)
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return None
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os.replace(tmp, dest)
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return dest
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def deposition(pdb_id, cache_dir):
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"""Coordinates path and the published refinement statistics, cached as <id>.json."""
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os.makedirs(cache_dir, exist_ok=True)
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meta_path = os.path.join(cache_dir, pdb_id + ".json")
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xyz = fetch(RCSB + pdb_id + ".cif.gz", os.path.join(cache_dir, pdb_id + ".cif.gz"))
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if xyz is None:
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return None
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if os.path.exists(meta_path):
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return json.load(open(meta_path))
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meta = refinement_record(pdb_id, xyz)
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json.dump(meta, open(meta_path, "w"), indent=1)
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return meta
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def refinement_record(name, xyz):
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"""The refinement statistics an mmCIF coordinate file states about itself (_refine)."""
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block = gemmi.cif.read(xyz).sole_block()
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methods = [m.strip("'\"") for m in block.find_values("_exptl.method")]
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rows = block.find("_refine.", ["pdbx_refine_id", "?ls_R_factor_R_free", "?ls_R_factor_R_work",
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"?ls_d_res_high"])
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ref = {}
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for row in rows: # a joint X-ray/neutron entry has one row per method; take the X-ray one
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if "X-RAY" in row.str(0).upper():
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ref = {k: (float(row[i]) if row.has(i) and gemmi.cif.is_null(row[i]) is False else None)
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for k, i in (("rfree", 1), ("rwork", 2), ("dmin", 3))}
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return {"id": name, "methods": methods, "rfree": ref.get("rfree"), "rwork": ref.get("rwork"),
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"dmin": ref.get("dmin"), "xyz": xyz}
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# ------------------------------------------------------------------ lattice / setting matching
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def metric(cell):
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a, b, c, al, be, ga = cell.parameters
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ca, cb, cg = np.cos(np.radians([al, be, ga]))
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return np.array([[a * a, a * b * cg, a * c * cb],
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[a * b * cg, b * b, b * c * ca],
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[a * c * cb, b * c * ca, c * c]])
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def niggli(cell, sg):
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"""Matrix M with (reduced primitive basis) = (conventional basis) @ M, and the reduced cell."""
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gv = gemmi.GruberVector(cell, sg.centring_type(), True)
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gv.niggli_reduce()
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op = gv.change_of_basis
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return np.array(op.rot, float) / op.DEN, gv.get_cell()
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UNIMODULAR = np.array([u for u in itertools.product((-1, 0, 1), repeat=9)
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if round(np.linalg.det(np.reshape(u, (3, 3)))) == 1], float).reshape(-1, 3, 3)
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def basis_changes(cell_d, sg_d, cell_m, sg_m):
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"""Every T (hkl_model = hkl_data @ T) whose lattice matches the model's, one per distinct
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reindexing modulo the model's point group (the member nearest the identity names it)."""
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md, red_d = niggli(cell_d, sg_d)
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mm, red_m = niggli(cell_m, sg_m)
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gd, gm = metric(red_d), metric(red_m)
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g = np.einsum("nji,jk,nkl->nil", UNIMODULAR, gd, UNIMODULAR)
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lengths = np.sqrt(np.einsum("nii->ni", g))
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lm = np.sqrt(np.diag(gm))
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ok = np.all(np.abs(lengths / lm - 1) < CELL_TOL, axis=1)
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cos = lambda g_, i, j, l_: g_[..., i, j] / (l_[..., i] * l_[..., j])
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for i, j in ((1, 2), (0, 2), (0, 1)):
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ang = np.degrees(np.arccos(np.clip(cos(g, i, j, lengths), -1, 1)))
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ok &= np.abs(ang - np.degrees(np.arccos(cos(gm, i, j, lm)))) < ANGLE_TOL
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asu, gops = gemmi.ReciprocalAsu(sg_m), sg_m.operations()
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probe = np.array([[1, 2, 3], [3, 1, 7], [5, 11, 2]]) * 12
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found = {}
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for u in UNIMODULAR[ok]:
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t = md @ u @ np.linalg.inv(mm)
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key = tuple(tuple(asu.to_asu([int(round(x)) for x in h], gops)[0]) for h in probe @ t)
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key = tuple(sorted(key))
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if key not in found or np.abs(t - np.eye(3)).sum() < np.abs(found[key] - np.eye(3)).sum():
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found[key] = t
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return list(found.values())
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def op_string(t):
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"""hkl_model = hkl_data @ T written as the usual h,k,l triplet."""
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from fractions import Fraction
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out = []
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for j in range(3):
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terms = ""
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for i, name in enumerate("hkl"):
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f = Fraction(t[i, j]).limit_denominator(12)
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if f == 0:
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continue
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sign = "-" if f < 0 else ("+" if terms else "")
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mag = abs(f)
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terms += sign + (name if mag == 1 else f"{mag}{name}" if mag.denominator == 1
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else f"{mag.numerator}{name}/{mag.denominator}")
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out.append(terms)
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return ",".join(out)
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# ------------------------------------------------------------------ reflection data
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def hkl_key(hkl):
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h = hkl.astype(np.int64) + 1024
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return (h[:, 0] * 2048 + h[:, 1]) * 2048 + h[:, 2]
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def to_group(hkl, f, sigf, flags, cell, sg, src):
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"""Reduce reflections to the asymmetric unit of sg; independent measurements of one
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reflection are averaged (1/sigma^2), copies of the same one (same `src`) are not. A reflection
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is free if any contributor is."""
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mtz = gemmi.Mtz()
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mtz.spacegroup, mtz.cell = sg, cell
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mtz.add_dataset("d")
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for lab, typ in (("H", "H"), ("K", "H"), ("L", "H"), ("S", "R")):
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mtz.add_column(lab, typ)
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mtz.set_data(np.column_stack([hkl, np.arange(len(hkl))]).astype(np.float32))
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mtz.ensure_asu()
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a = np.array(mtz, copy=False)
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order = a[:, 3].astype(np.int64)
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hkl, f, sigf, flags, src = a[:, :3].astype(int), f[order], sigf[order], flags[order], src[order]
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keep = ~sg.operations().systematic_absences(hkl)
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hkl, f, sigf, flags, src = hkl[keep], f[keep], sigf[keep], flags[keep], src[keep]
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key = hkl_key(hkl)
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_, first = np.unique(np.column_stack([key, src]), axis=0, return_index=True)
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hkl, f, sigf, flags, key = hkl[first], f[first], sigf[first], flags[first], key[first]
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_, idx, inv = np.unique(key, return_index=True, return_inverse=True)
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w = 1.0 / np.maximum(sigf, 1e-6) ** 2
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sw = np.bincount(inv, w)
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fm = np.bincount(inv, w * f) / sw
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flag = np.minimum.reduceat(flags[np.argsort(inv, kind="stable")],
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np.r_[0, np.cumsum(np.bincount(inv))[:-1]])
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return hkl[idx], fm, 1.0 / np.sqrt(sw), flag
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def read_rugnux(mtz_path):
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mtz = gemmi.read_mtz_file(mtz_path)
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labels = mtz.column_labels()
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need = ("F", "SIGF", "FreeR_flag")
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if not all(l in labels for l in need):
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raise RuntimeError(f"MTZ lacks one of {need}")
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return mtz
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def expand_p1(mtz):
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"""Rugnux's merge expanded to P1 (one hemisphere), with each row's source index."""
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m = gemmi.Mtz()
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m.spacegroup, m.cell = mtz.spacegroup, mtz.cell
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m.add_dataset("d")
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for lab, typ in (("H", "H"), ("K", "H"), ("L", "H"), ("S", "R")):
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m.add_column(lab, typ)
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m.set_data(np.column_stack([mtz.make_miller_array(), np.arange(mtz.nreflections)]).astype(np.float32))
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m.expand_to_p1()
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a = np.array(m, copy=False)
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return a[:, :3].astype(int), a[:, 3].astype(int)
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def reindexed(mtz, t, cell_m, sg_m):
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f = np.array(mtz.column_with_label("F"), copy=False).astype(float)
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s = np.array(mtz.column_with_label("SIGF"), copy=False).astype(float)
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fl = np.array(mtz.column_with_label("FreeR_flag"), copy=False).astype(int)
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good = np.isfinite(f) & np.isfinite(s) & (s > 0)
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hkl, src = expand_p1(mtz)
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hm = hkl @ t
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integral = np.all(np.abs(hm - np.round(hm)) < 1e-3, axis=1) & good[src]
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hm, src = np.round(hm[integral]).astype(int), src[integral]
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return to_group(hm, f[src], s[src], fl[src], cell_m, sg_m, src), integral.mean()
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def fcalc(st, d_min):
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dc = gemmi.DensityCalculatorX()
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dc.d_min = d_min
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dc.grid.setup_from(st)
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dc.set_refmac_compatible_blur(st[0])
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dc.put_model_density_on_grid(st[0])
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asu = gemmi.transform_map_to_f_phi(dc.grid).prepare_asu_data(dmin=d_min, unblur=dc.blur)
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return asu.miller_array, np.abs(asu.value_array)
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def shell_r(hkl, fo, fc_hkl, fc, cell, d_lo, d_hi):
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"""R after an overall scale and B, on the shell used only to choose the setting (low
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resolution excluded: unmodelled bulk solvent dominates there)."""
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_, i, j = np.intersect1d(hkl_key(hkl), hkl_key(fc_hkl), return_indices=True)
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fo, fc = fo[i], fc[j]
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d = cell.calculate_d_array(hkl[i])
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sel = (d <= d_lo) & (d >= d_hi) & (fo > 0) & (fc > 0)
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if sel.sum() < 50:
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return None
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fo, fc, s2 = fo[sel], fc[sel], 1.0 / d[sel] ** 2
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slope, lnk = np.polyfit(s2, np.log(fo / fc), 1)
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fm = np.exp(lnk + slope * s2) * fc
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return float(np.sum(np.abs(fo - fm)) / np.sum(fo))
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# ------------------------------------------------------------------ REFMAC
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_ENV = None
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def ccp4_env():
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global _ENV
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if _ENV is None:
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out = subprocess.run(["bash", "-c", f"source {CCP4_SETUP} >/dev/null 2>&1; env -0"],
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capture_output=True).stdout
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_ENV = dict(kv.split("=", 1) for kv in out.decode().split("\0") if "=" in kv)
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return _ENV
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def make_mtz(hkl, f, sigf, flags, cell, sg, dep_flags=None, labels=("F", "SIGF")):
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mtz = gemmi.Mtz(with_base=True)
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mtz.spacegroup, mtz.cell = sg, cell
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mtz.add_dataset("data")
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cols = [hkl.astype(float), f, sigf, flags]
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types = ("F", "Q") if labels[0] == "F" else ("J", "Q")
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for lab, typ in ((labels[0], types[0]), (labels[1], types[1]), ("FreeR_flag", "I")):
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mtz.add_column(lab, typ)
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if dep_flags is not None:
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mtz.add_column("FreeR_dep", "I")
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cols.append(dep_flags)
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mtz.set_data(np.column_stack(cols).astype(np.float32))
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return mtz
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def run_refmac(workdir, tag, mtz, xyz, keywords):
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"""REFMAC's R-work and R-free as it prints them, one per cycle."""
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log = os.path.join(workdir, tag + ".log")
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with open(log, "w") as fh:
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subprocess.run(["refmac5", "hklin", mtz, "xyzin", xyz,
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"hklout", os.path.join(workdir, tag + "_out.mtz"),
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"xyzout", os.path.join(workdir, tag + "_out.pdb")],
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input=keywords.encode(), stdout=fh, stderr=subprocess.STDOUT,
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cwd=workdir, env=ccp4_env())
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text = open(log, errors="replace").read()
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rw = [float(x) for x in re.findall(r"^Overall R factor\s+=\s+([\d.]+)", text, re.M)]
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rf = [float(x) for x in re.findall(r"^Free R factor\s+=\s+([\d.]+)", text, re.M)]
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if not rw or not rf:
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err = [l.strip() for l in text.splitlines() if "ERROR" in l.upper() or "Stop" in l
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or "Problem" in l or "does not seem" in l]
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raise RuntimeError("REFMAC gave no R factors: " + (err[-1] if err else "see " + log))
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return rw, rf
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def refmac(workdir, tag, mtz, xyz, d_min, free_label="FreeR_flag", twin=False):
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"""R-work, R-free of the model as given: the first cycle of REFMAC's rigid body, whose
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R-factors come before any shift is applied (bulk solvent + anisotropic overall scale are
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REFMAC's defaults). With `twin`, REFMAC finds the twin operators and fractions itself."""
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rw, rf = run_refmac(workdir, tag, mtz, xyz,
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f"labin FP=F SIGFP=SIGF FREE={free_label}\nrefi type rigid\nrigid ncycle 1\n"
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+ ("twin\n" if twin else "") + f"reso 999 {d_min:.3f}\nend\n")
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return rw[0], rf[0]
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def refine(workdir, tag, mtz, xyz, twin=False):
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"""R-work, R-free after REFMAC's restrained refinement of the model, over the data's whole
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resolution range: REFINE_CYCLES cycles, automatic weight, isotropic B for every atom (a
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deposited ANISOU is often TLS-derived, and refining it atom by atom diverged: -LL rising every
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cycle at 1.4 A on a model deposited at 1.7 A); a ligand without a dictionary entry gets REFMAC's
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own restraints instead of stopping the run."""
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rw, rf = run_refmac(workdir, tag, mtz, xyz,
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f"labin FP=F SIGFP=SIGF FREE=FreeR_flag\nncyc {REFINE_CYCLES}\nweight auto\n"
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"refi bref iso\nmake newligand continue\nmake check none\n"
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+ ("twin\n" if twin else "") + "end\n")
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return rw[-1], rf[-1]
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def rename_misfit_ligands(workdir, tag, xyz):
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"""A model whose ligand carries a CCD code that REFMAC's monomer library describes with other
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atoms ("atom ... is absent in the library": a code reused for another compound, or a model
|
|
built with its own) stops a restrained refinement. Such a residue is given a code the library
|
|
does not have, so REFMAC makes its restraints from the model's own coordinates, as for any new
|
|
ligand. Returns the renamed model and a note, or None when that is not the failure."""
|
|
log = open(os.path.join(workdir, tag + ".log"), errors="replace").read()
|
|
names = sorted(set(re.findall(r"ERROR : atom :\S+\s+(\S+)\s.*is absent in the library", log)))
|
|
if not names:
|
|
return None
|
|
lib = ccp4_env().get("CLIBD_MON", "")
|
|
free = (c for c in ("".join(t) for t in itertools.product("DQX", "0123456789", "0123456789"))
|
|
if not os.path.exists(os.path.join(lib, c[0].lower(), c + ".cif")))
|
|
new = {n: next(free) for n in names}
|
|
st = gemmi.read_structure(xyz)
|
|
for ch in st[0]:
|
|
for res in ch:
|
|
if res.name in new:
|
|
res.name = new[res.name]
|
|
out = os.path.join(workdir, "model_ligands_renamed.pdb")
|
|
st.write_pdb(out)
|
|
return out, ", ".join(f"{k}->{v}" for k, v in new.items())
|
|
|
|
|
|
def asu_key(hkl, sg):
|
|
"""hkl_key of the reflections mapped into gemmi's asymmetric unit (REFMAC writes its output
|
|
in its own convention, which is not always the same one)."""
|
|
asu, ops = gemmi.ReciprocalAsu(sg), sg.operations()
|
|
return hkl_key(np.array([asu.to_asu([int(x) for x in h], ops)[0] for h in hkl]).reshape(-1, 3))
|
|
|
|
|
|
def refined_shared(workdir, data, dep, cell_m, sg_m, xyz, twin):
|
|
"""Both data sets refined from the deposited model by the same protocol, each over its own
|
|
resolution range, and R-free on a SHARED free set: the depositor's free reflections present in
|
|
both data sets. Depositor free reflections outside that intersection are removed from both, so
|
|
neither refinement uses a free reflection as a work reflection; every other reflection of a
|
|
data set is a work reflection of that data set."""
|
|
hkl, f, s = data
|
|
hkl_d, f_d, s_d, flags_d = dep
|
|
k, k_d = asu_key(hkl, sg_m), asu_key(hkl_d, sg_m)
|
|
shared = np.intersect1d(k_d[flags_d == 0], k)
|
|
keep_d = (flags_d != 0) | np.isin(k_d, shared)
|
|
free = np.isin(k, shared)
|
|
out = {"shared_free_n": int(len(shared))}
|
|
tags = (("", hkl, f, s, free, "data_refine.mtz"),
|
|
("_depdata", hkl_d[keep_d], f_d[keep_d], s_d[keep_d], flags_d[keep_d] == 0,
|
|
"deposited_refine.mtz"))
|
|
for suffix, h, fo, so, fr, name in tags:
|
|
mtz = os.path.join(workdir, name)
|
|
make_mtz(h, fo, so, np.where(fr, 0, 1), cell_m, sg_m).write_to_file(mtz)
|
|
tag = "refine" + (suffix or "_rugnux")
|
|
try:
|
|
r = refine(workdir, tag, mtz, xyz, twin)
|
|
except RuntimeError:
|
|
renamed = rename_misfit_ligands(workdir, tag, xyz)
|
|
if renamed is None:
|
|
raise
|
|
xyz, out["ligands_renamed"] = renamed
|
|
r = refine(workdir, tag, mtz, xyz, twin)
|
|
out["refined_rwork" + suffix], out["refined_rfree_refmac" + suffix] = r
|
|
# REFMAC's own R-free is over exactly the shared set: it is both data sets' free set. Not
|
|
# recomputed from the output MTZ - its F carries REFMAC's anisotropic scale, which on
|
|
# strongly anisotropic data blows up the weak direction's noise and inflates R
|
|
out["refined_rfree_shared" + suffix] = out["refined_rfree_refmac" + suffix]
|
|
return {k_: (round(v, 4) if isinstance(v, float) else v) for k_, v in out.items()}
|
|
|
|
|
|
def read_model(xyz):
|
|
"""The deposited model with its strict-NCS copies generated: an entry can hold part of the
|
|
asymmetric unit and the operators that make the rest (_struct_ncs_oper 'generate', MTRIX without
|
|
the given flag) - an icosahedral virus deposits a few chains of dozens."""
|
|
st = gemmi.read_structure(xyz)
|
|
if any(not op.given for op in st.ncs):
|
|
st.expand_ncs(gemmi.HowToNameCopiedChain.Short)
|
|
return st
|
|
|
|
|
|
def model_for_refmac(st, workdir):
|
|
"""The deposited model written in a form REFMAC reads, unchanged in everything it scores;
|
|
returns the file and what had to be changed ("none" normally)."""
|
|
st = st.clone()
|
|
st.setup_entities()
|
|
changes = []
|
|
# An atom of unknown element (UNX, element X) stops REFMAC outright ("Atom does not seem to be
|
|
# an atom"); it has no scattering factor, so leaving it out loses nothing REFMAC could use.
|
|
unknown = 0
|
|
for ch in st[0]:
|
|
for i in reversed(range(len(ch))):
|
|
for k in reversed(range(len(ch[i]))):
|
|
if ch[i][k].element == gemmi.Element("X"):
|
|
del ch[i][k]
|
|
unknown += 1
|
|
if len(ch[i]) == 0:
|
|
del ch[i]
|
|
if unknown:
|
|
st.remove_empty_chains()
|
|
changes.append(f"{unknown} atoms of unknown element dropped")
|
|
# PDB format wherever it can hold the model: REFMAC's mmCIF reader rejects many models whose
|
|
# atoms carry ANISOU only in part ("rdaniso_cif: Atom symbol mismatch"), while in the PDB format
|
|
# each ANISOU follows its own ATOM line. Chain names longer than two characters (e.g. 'AAA')
|
|
# are what usually rules the PDB format out; renaming chains changes nothing REFMAC scores.
|
|
if any(len(ch.name) > 2 for ch in st[0]):
|
|
st.shorten_chain_names()
|
|
if st[0].count_atom_sites() < 100000 and all(len(ch.name) <= 2 for ch in st[0]):
|
|
xyz = os.path.join(workdir, "model.pdb")
|
|
st.write_pdb(xyz)
|
|
else:
|
|
# too large for the PDB format: mmCIF with isotropic B only, which REFMAC reads reliably
|
|
# (B_iso holds B_eq for an anisotropic atom)
|
|
for ch in st[0]:
|
|
for res in ch:
|
|
for atom in res:
|
|
atom.aniso = gemmi.SMat33f(0, 0, 0, 0, 0, 0)
|
|
xyz = os.path.join(workdir, "model.cif")
|
|
st.make_mmcif_document().write_file(xyz)
|
|
changes.append("ANISOU dropped (mmCIF)")
|
|
return xyz, "; ".join(changes) or "none"
|
|
|
|
|
|
# ------------------------------------------------------------------ depositor's structure factors
|
|
|
|
def refln_value(b, labels, value, sigma, plus, minus):
|
|
"""A value and its sigma per reflection, and where they came from: the columns
|
|
`value`/`sigma`, else the mean of the Friedel pair `plus`/`minus` (either member alone where
|
|
the other is missing); None if the block has neither."""
|
|
if value in labels and sigma in labels:
|
|
return b.make_float_array(value), b.make_float_array(sigma), value
|
|
if not all(x in labels for x in (plus, plus + "_sigma", minus, minus + "_sigma")):
|
|
return None
|
|
vp, sp = b.make_float_array(plus), b.make_float_array(plus + "_sigma")
|
|
vm, sm = b.make_float_array(minus), b.make_float_array(minus + "_sigma")
|
|
both, p_only = np.isfinite(vp) & np.isfinite(vm), np.isfinite(vp) & ~np.isfinite(vm)
|
|
v = np.where(both, (vp + vm) / 2, np.where(p_only, vp, vm))
|
|
s = np.where(both, np.sqrt(sp ** 2 + sm ** 2) / 2, np.where(p_only, sp, sm))
|
|
return v, s, f"mean of {plus}/{minus}"
|
|
|
|
|
|
def french_wilson(workdir, hkl, i, sigi, flags, cell, sg):
|
|
"""Amplitudes from merged intensities by ctruncate (French & Wilson), as the depositor's own
|
|
CCP4 route would have made them."""
|
|
hklin = os.path.join(workdir, "deposited_i.mtz")
|
|
hklout = os.path.join(workdir, "deposited_fw.mtz")
|
|
make_mtz(hkl, i, sigi, flags, cell, sg, labels=("I", "SIGI")).write_to_file(hklin)
|
|
with open(os.path.join(workdir, "ctruncate.log"), "w") as fh:
|
|
subprocess.run(["ctruncate", "-hklin", hklin, "-hklout", hklout, "-colin", "/*/*/[I,SIGI]",
|
|
"-freein", "/*/*/[FreeR_flag]"],
|
|
stdout=fh, stderr=subprocess.STDOUT, cwd=workdir, env=ccp4_env())
|
|
if not os.path.exists(hklout):
|
|
raise RuntimeError("ctruncate failed: see " + os.path.join(workdir, "ctruncate.log"))
|
|
out = gemmi.read_mtz_file(hklout)
|
|
col = lambda lab: np.array(out.column_with_label(lab), copy=False).astype(float)
|
|
return out.make_miller_array(), col("F"), col("SIGF"), col("FreeR_flag").astype(int)
|
|
|
|
|
|
def depositor_data(pdb_id, cache_dir, workdir, cell_m, sg_m):
|
|
"""The first reflection block of the entry's -sf.cif as an MTZ (F, SIGF, FreeR_flag) in the
|
|
model's cell and group, and what the amplitudes were made from. Amplitudes: F_meas, else the
|
|
mean of F(+)/F(-); where only intensities were deposited (I, else the mean of I(+)/I(-)) they
|
|
are converted by French-Wilson. Free flags from _refln.status ('f' free), else from a numeric
|
|
_refln.pdbx_r_free_flag (0 when it takes more than two values - the CCP4 convention - else the
|
|
minority value). Returns None, reason when there is nothing usable."""
|
|
path = fetch(RCSB + pdb_id + "-sf.cif.gz", os.path.join(cache_dir, pdb_id + "-sf.cif.gz"))
|
|
if path is None:
|
|
return None, "no deposited structure factors"
|
|
rb = gemmi.as_refln_blocks(gemmi.cif.read(path))
|
|
if not rb:
|
|
return None, "no reflection block"
|
|
b = rb[0]
|
|
labels = b.column_labels()
|
|
hkl = b.make_miller_array()
|
|
val = refln_value(b, labels, "F_meas_au", "F_meas_sigma_au", "pdbx_F_plus", "pdbx_F_minus")
|
|
amplitudes = val is not None
|
|
if not amplitudes:
|
|
val = refln_value(b, labels, "intensity_meas", "intensity_sigma", "pdbx_I_plus", "pdbx_I_minus")
|
|
if val is None:
|
|
return None, "deposited structure factors carry neither amplitudes nor intensities"
|
|
f, s, kind = val
|
|
status = np.array([x.strip("'\"") for x in b.block.find_values("_refln.status")]) \
|
|
if "status" in labels else np.array([])
|
|
if len(status) == len(hkl) and np.any(status == "f"):
|
|
use = (status == "f") | (status == "o")
|
|
flags = np.where(status == "f", 0, 1)
|
|
elif "pdbx_r_free_flag" in labels:
|
|
v = b.make_int_array("pdbx_r_free_flag", -1)
|
|
vals, counts = np.unique(v[v >= 0], return_counts=True)
|
|
if len(vals) < 2:
|
|
return None, "deposited structure factors carry no free set"
|
|
free = 0 if len(vals) > 2 and 0 in vals else vals[np.argmin(counts)]
|
|
use = v >= 0
|
|
flags = np.where(v == free, 0, 1)
|
|
else:
|
|
return None, "deposited structure factors carry no free set"
|
|
use &= np.isfinite(f) & np.isfinite(s) & (s > 0)
|
|
if not np.allclose(b.cell.parameters, cell_m.parameters, rtol=0.02, atol=0.5):
|
|
return None, "deposited structure factors in another cell"
|
|
hkl, f, s, flags = to_group(hkl[use], f[use], s[use], flags[use], cell_m, sg_m,
|
|
np.arange(use.sum()))
|
|
if not amplitudes:
|
|
hkl, f, s, flags = french_wilson(workdir, hkl, f, s, flags, cell_m, sg_m)
|
|
kind += ", French-Wilson (ctruncate)"
|
|
return (make_mtz(hkl, f, s, flags, cell_m, sg_m), kind), None
|
|
|
|
|
|
def declared_twin(xyz):
|
|
"""The twin operators the entry declares (_pdbx_reflns_twin), [] when it declares none."""
|
|
block = gemmi.cif.read(xyz).sole_block()
|
|
ops = [o.strip("'\"").replace(" ", "").upper()
|
|
for o in block.find_values("_pdbx_reflns_twin.operator")]
|
|
return ops if len(ops) > 1 else []
|
|
|
|
|
|
def choose_setting(mtz, fc_hkl, fc, cell_m, sg_m, d_lo, d_hi):
|
|
"""Every change of basis carrying the data's lattice onto the model's, as (shell R, fraction
|
|
indexed, T, reflections in the model's setting), best agreement with the model's Fcalc first."""
|
|
scored = []
|
|
for t in basis_changes(mtz.cell, mtz.spacegroup, cell_m, sg_m):
|
|
data, frac = reindexed(mtz, t, cell_m, sg_m)
|
|
r = shell_r(data[0], data[1], fc_hkl, fc, cell_m, d_lo, d_hi)
|
|
if r is not None:
|
|
scored.append((r, frac, t, data))
|
|
return sorted(scored, key=lambda x: x[0])
|
|
|
|
|
|
# ------------------------------------------------------------------ the check
|
|
|
|
def check(mtz_path, pdb_id, workdir, cache_dir=DEFAULT_CACHE, baseline=True, refined=True):
|
|
t0 = time.time()
|
|
res = {"status": "failed", "reason": "", "rwork": None, "rfree": None,
|
|
"rfree_deposited": None, "rwork_deposited": None, "d_min_used": None, "sg_used": None,
|
|
"reindex_op": None, "cycles": 0, "seconds": None,
|
|
"rfree_depflags": None,
|
|
"rwork_depdata": None, "rfree_depdata": None, "baseline_note": None,
|
|
"depdata_kind": None, "reindex_op_depdata": None, "twin_declared": None,
|
|
"refined_rwork": None, "refined_rfree_shared": None, "refined_rfree_refmac": None,
|
|
"refined_rwork_depdata": None, "refined_rfree_shared_depdata": None,
|
|
"refined_rfree_refmac_depdata": None, "shared_free_n": None, "refined_reason": None,
|
|
"sg_data": None, "d_min_data": None, "d_min_deposited": None, "cell_diff_pct": None,
|
|
"setting_r": None, "setting_r_next": None, "fraction_indexed": None,
|
|
"model_modification": "none", "protocol": "REFMAC R-factors of the model as deposited, bulk solvent, no refinement"}
|
|
|
|
def done(status, reason=""):
|
|
res["status"], res["reason"] = status, reason
|
|
res["seconds"] = round(time.time() - t0, 1)
|
|
return res
|
|
|
|
pdb_id = pdb_id.lower()
|
|
if not PDB_ID.match(pdb_id):
|
|
return done("n/a", "not a PDB entry (small molecule or unpublished set)")
|
|
try:
|
|
workdir = os.path.abspath(workdir) # REFMAC runs inside it
|
|
os.makedirs(workdir, exist_ok=True)
|
|
meta = deposition(pdb_id, cache_dir)
|
|
if meta is None:
|
|
return done("failed", "entry could not be downloaded")
|
|
res["rfree_deposited"], res["rwork_deposited"] = meta["rfree"], meta["rwork"]
|
|
res["d_min_deposited"] = meta["dmin"]
|
|
if not any("X-RAY" in m.upper() for m in meta["methods"]):
|
|
return done("n/a", "not an X-ray structure: " + ", ".join(meta["methods"]))
|
|
if meta["rfree"] is None:
|
|
return done("n/a", "no deposited R-free")
|
|
st = read_model(meta["xyz"])
|
|
if len(st) > 1:
|
|
return done("skipped", f"{len(st)} models in the entry")
|
|
natoms = st[0].count_atom_sites()
|
|
if natoms > MAX_ATOMS:
|
|
return done("skipped", f"{natoms} atoms, above {MAX_ATOMS}")
|
|
sg_m, cell_m = st.find_spacegroup(), st.cell
|
|
if sg_m is None:
|
|
return done("failed", f"model space group '{st.spacegroup_hm}' not recognised")
|
|
|
|
mtz = read_rugnux(mtz_path)
|
|
res["sg_data"] = mtz.spacegroup.hm
|
|
res["d_min_data"] = round(mtz.resolution_high(), 3)
|
|
d_used = max(mtz.resolution_high(), meta["dmin"] or 0)
|
|
res["d_min_used"] = round(d_used, 3)
|
|
res["sg_used"] = sg_m.hm
|
|
|
|
# choose the setting on a mid-resolution shell against the model's Fcalc
|
|
d_hi = max(3.0, d_used)
|
|
d_lo = max(8.0, 1.6 * d_hi)
|
|
fc_hkl, fc = fcalc(st, d_hi)
|
|
scored = choose_setting(mtz, fc_hkl, fc, cell_m, sg_m, d_lo, d_hi)
|
|
if not scored:
|
|
return done("failed", "no change of basis carries the data lattice onto the model's")
|
|
r_best, frac, t, (hkl, f, s, fl) = scored[0]
|
|
res["setting_r"] = round(r_best, 4)
|
|
res["setting_r_next"] = round(scored[1][0], 4) if len(scored) > 1 else None
|
|
res["fraction_indexed"] = round(float(frac), 4)
|
|
res["reindex_op"] = op_string(t)
|
|
gd = t.T @ metric(mtz.cell) @ t
|
|
res["cell_diff_pct"] = round(100 * float(np.max(np.abs(
|
|
np.sqrt(np.diag(gd)) / np.array(cell_m.parameters[:3]) - 1))), 2)
|
|
|
|
# the depositor's data go through the same setting choice: their indexing can be the
|
|
# other branch of a merohedral ambiguity (a twinned entry refined in its minor domain's)
|
|
dep = None
|
|
if baseline:
|
|
dep, why = depositor_data(pdb_id, cache_dir, workdir, cell_m, sg_m)
|
|
res["baseline_note"] = why
|
|
dep_flags = None
|
|
if dep is not None:
|
|
dep_mtz, res["depdata_kind"] = dep
|
|
dep_scored = choose_setting(dep_mtz, fc_hkl, fc, cell_m, sg_m, d_lo, d_hi)
|
|
if dep_scored:
|
|
res["reindex_op_depdata"] = op_string(dep_scored[0][2])
|
|
dep = dep_scored[0][3]
|
|
_, i, j = np.intersect1d(hkl_key(hkl), hkl_key(dep[0]), return_indices=True)
|
|
dep_flags = np.full(len(hkl), 1) # absent from the deposited set -> work
|
|
dep_flags[i] = dep[3][j]
|
|
else:
|
|
dep, res["baseline_note"] = None, "deposited structure factors too few to place"
|
|
data_mtz = os.path.join(workdir, "data.mtz")
|
|
make_mtz(hkl, f, s, fl, cell_m, sg_m, dep_flags).write_to_file(data_mtz)
|
|
xyz, res["model_modification"] = model_for_refmac(st, workdir)
|
|
if dep is not None:
|
|
dep_mtz = os.path.join(workdir, "deposited.mtz")
|
|
make_mtz(*dep, cell_m, sg_m).write_to_file(dep_mtz)
|
|
|
|
def score(twin, suffix):
|
|
out = {}
|
|
out["rwork"], out["rfree"] = refmac(workdir, "rugnux" + suffix, data_mtz, xyz, d_used,
|
|
twin=twin)
|
|
if dep is not None:
|
|
out["rfree_depflags"] = refmac(workdir, "rugnux_depflags" + suffix, data_mtz, xyz,
|
|
d_used, "FreeR_dep", twin=twin)[1]
|
|
out["rwork_depdata"], out["rfree_depdata"] = refmac(workdir, "deposited" + suffix,
|
|
dep_mtz, xyz, d_used, twin=twin)
|
|
return {k: round(v, 4) for k, v in out.items()}
|
|
|
|
# An entry refined as a twin is scored as one, both data sets alike: its published R-free
|
|
# is a twinned one, and an untwinned score of twinned data says more about the twin
|
|
# fraction than about the data. The untwinned numbers are kept beside it.
|
|
res["twin_declared"] = declared_twin(meta["xyz"]) or None
|
|
res.update(score(bool(res["twin_declared"]), ""))
|
|
if res["twin_declared"]:
|
|
res["protocol"] += ", REFMAC twin refinement (the entry declares twinning)"
|
|
res["untwinned"] = score(False, "_untwinned")
|
|
if dep is not None and refined:
|
|
try:
|
|
res.update(refined_shared(workdir, (hkl, f, s), dep, cell_m, sg_m, xyz,
|
|
bool(res["twin_declared"])))
|
|
except Exception as e: # the first-cycle numbers stand without it
|
|
if os.environ.get("MODEL_CHECK_RAISE"):
|
|
raise
|
|
res["refined_reason"] = f"{type(e).__name__}: {e}"
|
|
return done("ok")
|
|
except Exception as e: # one bad entry must not stop a battery
|
|
if os.environ.get("MODEL_CHECK_RAISE"):
|
|
raise
|
|
return done("failed", f"{type(e).__name__}: {e}")
|
|
|
|
|
|
def main():
|
|
ap = argparse.ArgumentParser(description=__doc__.split("\n\n")[0])
|
|
ap.add_argument("mtz", help="Rugnux merged MTZ (needs F, SIGF, FreeR_flag)")
|
|
ap.add_argument("pdb_id")
|
|
ap.add_argument("--workdir", default=None, help="default: model_check_<id> beside the MTZ")
|
|
ap.add_argument("--cache", default=DEFAULT_CACHE)
|
|
ap.add_argument("--no-baseline", action="store_true",
|
|
help="skip the depositor's structure factors")
|
|
ap.add_argument("--no-refine", action="store_true",
|
|
help="first-cycle R factors only (skip the refined shared-free-set protocol)")
|
|
a = ap.parse_args()
|
|
wd = a.workdir or os.path.join(os.path.dirname(os.path.abspath(a.mtz)), "model_check_" + a.pdb_id)
|
|
print(json.dumps(check(a.mtz, a.pdb_id, os.path.abspath(wd), a.cache, baseline=not a.no_baseline,
|
|
refined=not a.no_refine), indent=1))
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|