From ee016d3d130e9f5eb1e0fb70e5da82d623a30186 Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Wed, 21 Oct 2026 20:01:51 +0200 Subject: [PATCH] rugnux live maps: one unit cell centred on the model; the viewer opens on all of it /rugnux/map.ccp4 now serves one unit cell of map, centred on the model, instead of the model's box plus 5 A; along an axis where the model reaches further than the cell (a predicted model with long termini in a small cell), the model plus 5 A instead, so that all of it has density. The Mol* viewer opens on the whole cell and the model (map radius 0); a radius still draws the maps only around the centre of view, Coot-style. Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 1c1e1d96359f112d6820d972005e9f7eca4ebd50) --- broker/jfjoch_api.yaml | 6 ++-- broker/redoc-static.html | 8 +++--- docs/python_client/docs/DefaultApi.md | 6 ++-- .../src/client/@tanstack/react-query.gen.ts | 6 ++-- frontend/src/client/sdk.gen.ts | 6 ++-- .../src/components/RugnuxStructureViewer.tsx | 27 ++++++++++-------- receiver/RugnuxStructure.cpp | 11 +++++++- receiver/RugnuxStructure.h | 7 +++-- tests/RugnuxStructureTest.cpp | 28 +++++++++++++++---- 9 files changed, 69 insertions(+), 36 deletions(-) diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml index 416219559..265206dba 100644 --- a/broker/jfjoch_api.yaml +++ b/broker/jfjoch_api.yaml @@ -3641,9 +3641,9 @@ paths: summary: Get an electron-density map of the last rugnux live run description: | The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map - coefficients written to `_maps.mtz`. It covers the box around the model plus 5 A on every side, sampled - every d_min/3; the mean and RMS in its header are those of the whole unit cell, so contour levels in - sigma are the usual ones. + coefficients written to `_maps.mtz`. It covers one unit cell centred on the model - along an axis where + the model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and + RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones. parameters: - in: query name: type diff --git a/broker/redoc-static.html b/broker/redoc-static.html index 9e1fcf118..d346ae438 100644 --- a/broker/redoc-static.html +++ b/broker/redoc-static.html @@ -872,9 +872,9 @@ metadata (entities, sequences, references, authors, software) kept. Kept as long

Get an electron-density map of the last rugnux live run

The map of the placed model (/rugnux/model.cif) in CCP4 format (mode 2, float), made from the map -coefficients written to _maps.mtz. It covers the box around the model plus 5 A on every side, sampled -every d_min/3; the mean and RMS in its header are those of the whole unit cell, so contour levels in -sigma are the usual ones.

+coefficients written to _maps.mtz. It covers one unit cell centred on the model - along an axis where +the model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and +RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones.

Authorizations:
bearerAuth
query Parameters
type
string
Default: "2fofc"
Enum: "2fofc" "fofc"

2fofc: the 2mFo-DFc map; fofc: the mFo-DFc difference map

Responses