coot-NCS-reference-guidance

To fix sequence discrepancies between NCS-related chains in COOT, compare the related chains to identify inconsistencies, then use the best-built copy as a template to copy fragments and align sequences across symmetry-related copies.

NCS reference-guided rebuilding is a structure refinement technique that uses the best-built molecular copy as a template to ensure sequence and coordinate consistency across symmetry-related chains, reducing manual trial-and-error and build errors.

You copy fragments across NCS chains in COOT by using NCS transforms to apply coordinates from the template chain, changing chain IDs, and replacing fragments followed by iterative refinement with flanking residues.

Yes, you can use COOT scripting functions to automate NCS ghost comparisons, perform transformations, execute chain ID changes, replace fragments, and run iterative refinement to ensure sequence consistency across NCS-related copies.

The best way to refine symmetry-related molecules after copying NCS fragments is to perform targeted refinements using flanking residues during model rebuilding, ensuring coordinate consistency and improving overall model accuracy.

NCS copies have inconsistent coordinates after structure refinement when sequence discrepancies exist between related chains, requiring reference-guided rebuilding using the better-built chain as a template to copy fragments via NCS transforms.