mx/Jungfraujoch
3
2
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases 81 Wiki Activity

Merge branch 'mr-tncs-null' into rc175: --af-model null turns each copy about its own centroid, so tNCS no longer lets wrong models pass

Browse Source 
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-10-12 16:48:36 +02:00
co-authored by Claude Opus 5.5
parent 699bff1cb1 babff6d8bf
commit 1b21958828
1 changed files with 22 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files
image_analysis/structure_refinement/MolecularReplacement.cpp
+22 -11
View File
@@ -459,11 +459,14 @@ gemmi::Fractional centroid(const gemmi::Structure &st) {
// about its centroid, in standard deviations of the latter: the null model validation builds for a
// model that claims something (ModelValidation.cpp). An orientation the crystal cannot tell from the
// placement's - within the rigid body's reach of one of its symmetry classes - is drawn again.
// With several copies each is turned about its own centroid, all by the same rotation: the copies keep
// their arrangement, and with it the fit that tNCS gives any model placed parallel at its vector, so that
// only the model's own orientation is random.
// `translate`: where given, each replicate is placed where the translation function puts the model in its
// orientation (the centroids, fractional, of the model in each of the orientations given), as the search
// placed the real one, instead of at the real placement's centroid; the search chose that position among
// all others for the real orientation, and a null that is not given the same choice reads high.
double null_sigma(const gemmi::Structure &placed, const gemmi::Mat33 &orientation, const gemmi::SpaceGroup &sg,
double null_sigma(const gemmi::Structure &placed, int copies, const gemmi::Mat33 &orientation, const gemmi::SpaceGroup &sg,
const std::vector<MergedReflection> &merged, double d_min, RigidBodyGPUPool *pool,
size_t nthreads, ScoreEngines *scorers,
const std::function<std::vector<gemmi::Fractional>(const std::vector<gemmi::Mat33> &)> &translate) {
@@ -497,15 +500,23 @@ double null_sigma(const gemmi::Structure &placed, const gemmi::Mat33 &orientatio
workers.push_back(std::async(std::launch::async, [&] {
for (int i = next++; i < NULL_REPLICATES; i = next++) {
gemmi::Structure rep = placed;
std::vector<gemmi::Position> pos = ModelPositions(rep.models[0]);
gemmi::Vec3 c;
for (const gemmi::Position &p : pos)
c += p;
c *= 1.0 / static_cast<double>(pos.size());
const gemmi::Vec3 to = translate ? gemmi::Vec3(placed.cell.orthogonalize(where[i])) : c;
for (gemmi::Position &p : pos)
p = gemmi::Position(draws[i].multiply(gemmi::Vec3(p) - c) + to);
SetModelPositions(rep.models[0], pos);
std::vector<gemmi::Chain> &chains = rep.models[0].chains;
for (int k = 0; k < copies; k++) {
// Copy k: the chains SplitCopies gives it.
std::vector<gemmi::Atom *> atoms;
for (size_t ch = 0; ch < chains.size(); ch++)
if (static_cast<int>(ch * copies / chains.size()) == k)
for (gemmi::Residue &r : chains[ch].residues)
for (gemmi::Atom &a : r.atoms)
atoms.push_back(&a);
gemmi::Vec3 c;
for (const gemmi::Atom *a : atoms)
c += a->pos;
c *= 1.0 / static_cast<double>(atoms.size());
const gemmi::Vec3 to = translate ? gemmi::Vec3(placed.cell.orthogonalize(where[i])) : c;
for (gemmi::Atom *a : atoms)
a->pos = gemmi::Position(draws[i].multiply(gemmi::Vec3(a->pos) - c) + to);
}
r_work[i] = refine_placement(rep, sg, coarse, null_d_min, pool, nthreads, scorers).r_work;
}
}));
@@ -2440,7 +2451,7 @@ MolecularReplacementResult search_model(const SearchModel &model, const std::vec
out.push_back(p.t);
return out;
};
c.null_sigma = null_sigma(*c.placed, orientations[best], c.space_group, *merges[merge].merged,
c.null_sigma = null_sigma(*c.placed, c.copies, orientations[best], c.space_group, *merges[merge].merged,
result.d_min_score, engines.get(), nthreads, &scorers, translate);
result.t_null += seconds_since(t_null);
if (c.null_sigma >= NULL_SIGMA_MIN)