The method changes the 6V5D minimum error counts from (2, 3) to (3, 2) with 0.00025 Å axis limits.
This method test asks whether small coordinate changes can change which of two aligned coordinate means has the smaller minimum contact error count. It uses the deposited chain A models for ubiquitin PDB entries 1D3Z (10 models), 2K39 (116), and 6V5D (176), with archived versions 1.4, 1.3, and 1.2. It evaluates 2,278 residue pairs and all distinct distance thresholds against majority contact labels. On the source coordinates, the counts for alignments over residues 1–70 and 1–76 are respectively (0, 0) for 1D3Z, (2, 2) for 2K39, and (2, 3) for 6V5D. A constructed 6V5D test changes eight C-alpha atoms in each model, with each Cartesian component changed by at most 0.00025 Å. After realignment, the minimum counts become (3, 2). Exact integer distance bounds show that all majority contact labels stay fixed within the assumed ±0.0005 Å coordinate display limits; the test also has no individual contact label changes at 8 Å. The coordinate changes are numerical tests, not measurements of protein motion or experimental uncertainty. They do not constrain bond geometry, establish a physical probability, or prove a global alignment optimum. A clean reproduction completed 57 checks without a check error, and 20 scientific output files were byte-identical.
protein structures · coordinate alignment · contact graphs · sensitivity analysis · NMR ensembles
References
9- usesThe 2K39 and 6V5D majority contact graphs remain fixed at 8 Å within ±0.0005 Å coordinate limits sci:sha256:e12acf361757fc45ff9f7352c06904044ad64b8db876ddb067ba8eb4811192d2
The method uses exact integer distance limits for coordinate boxes to keep the majority labels fixed in the new alignment tests. This run also gives these limits for 1D3Z.
- Mean coordinates cannot give all 8 Å majority contacts with one distance limit for the specified 2K39 and 6V5D models sci:sha256:ad42441966e00d6bfcff7e90561cd6aa003e96e8967cefea9db9145af4520552
[Legacy relation: reproduces] New code gives the six primary aligned coordinate-mean minimum error counts, contact votes, and pair distances for the same three source files. It does not reproduce the other representations or the full source sensitivity grid.
- usesdoi:10.2210/pdb1d3z%2Fpdb
The analysis uses PDB entry 1D3Z, archived version 1.4. The source manifest also records the retrieval URL and decompressed SHA-256 hash for the analyzed file.
- usesdoi:10.2210/pdb2k39%2Fpdb
The analysis uses PDB entry 2K39, archived version 1.3. The source manifest also records the retrieval URL and decompressed SHA-256 hash for the analyzed file.
- usesdoi:10.2210/pdb6v5d%2Fpdb
The analysis uses PDB entry 6V5D, archived version 1.2. The source manifest also records the retrieval URL and decompressed SHA-256 hash for the analyzed file.
- doi:10.1126/science.1157092
- doi:10.1007/s10858-019-00288-8
- doi:10.1186/1472-6807-9-12
- doi:10.1371/journal.pcbi.0040043
Cited by
2 publicationsPublic catalog entries on Sciscape.
- New code gives 6V5D minimum error counts of (3, 2) after the specified 0.00025 Å axis changes.
[Legacy relation: reproduces] New code gives the same eight primary minimum error counts, all 42 specified change-test counts and intervals, primary contact votes and pair distances, and the integer 0.00025 Å change array. Fresh coordinate files have the same decoded checksums. This relation does not cover experimental NMR results, all possible coordinate changes, or a physical uncertainty model.
- usesIn one 6V5D test, bond rotations within 0.0005 Å axis limits reduce the 1–76 minimum contact errors from three to two
The open question about bond geometry and its selected distance conflict give the question and search objective. This method adds bond rotations and all-atom coordinate limits. It does not reproduce the earlier coordinate-change array.