Update of bug #22963 (project relax):
Status: None => Invalid
Open/Closed: Open => Closed
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Follow-up Comment #4:
The problem in this case was the PDB file
test_suite/shared_data/model_free/sphere/sphere.pdb. It has no CONECT records
and all the nitrogens are at [0, 0, 0]:
ATOM 1 N GLY 1 0.000 0.000 0.000 1.00 0.00
ATOM 2 H GLY 1 0.745 0.000 -0.667 1.00 0.00
ATOM 3 N GLY 2 0.000 0.000 0.000 1.00 0.00
ATOM 4 H GLY 2 -0.373 0.645 -0.667 1.00 0.00
ATOM 5 N GLY 3 0.000 0.000 0.000 1.00 0.00
ATOM 6 H GLY 3 -0.373 -0.645 -0.667 1.00 0.00
ATOM 7 N GLY 4 0.000 0.000 0.000 1.00 0.00
ATOM 8 H GLY 4 1.000 0.000 0.000 1.00 0.00
ATOM 9 N GLY 5 0.000 0.000 0.000 1.00 0.00
ATOM 10 H GLY 5 -0.500 0.866 0.000 1.00 0.00
ATOM 11 N GLY 6 0.000 0.000 0.000 1.00 0.00
ATOM 12 H GLY 6 -0.500 -0.866 0.000 1.00 0.00
ATOM 13 N GLY 7 0.000 0.000 0.000 1.00 0.00
ATOM 14 H GLY 7 0.745 0.000 0.667 1.00 0.00
ATOM 15 N GLY 8 0.000 0.000 0.000 1.00 0.00
ATOM 16 H GLY 8 -0.373 0.645 0.667 1.00 0.00
ATOM 17 N GLY 9 0.000 0.000 0.000 1.00 0.00
ATOM 18 H GLY 9 -0.373 -0.645 0.667 1.00 0.00
ATOM 19 NE1 GLY 9 0.000 0.000 0.000 1.00 0.00
ATOM 20 HE1 GLY 9 0.577 0.577 0.577 1.00 0.00
END
Therefore the algorithm for finding connected atoms within a 2 Angstrom radius
was failing to correctly identify the connectivities. The solution is to not
use such a strange structure, or to at least provide CONECT records.
Therefore the bug is being closed as invalid.
A proper solution would be to determine connectivities for proteins, RNA and
DNA based on the PDB fragment/residue definitions (where the residue name and
spin name are unambiguously defined).
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[bug #22963] Using '@N*' to define the interatomic interactions for a model-free analysis fails when using non-backbone 15N spins.