skills/smithery.ai/coot-model-building

coot-model-building

SKILL.md

Key Lessons from Chain A Refinement Session

Workflow Checklist - Follow This for Model-Building and Refimentment

Best practices for fixing any issue:

  1. ☐ Center on the interesting residue: coot.set_go_to_atom_chain_residue_atom_name(chain, resno, "CA") or interesting postion coot.set_rotation_centre(x,y,z)
  2. ☐ Check current metrics (Rama/correlation/overlaps)
  3. ☐ Make checkpoint if trying something experimental
  4. ☐ Apply fix
  5. ☐ Re-check metrics to confirm improvement
  6. ☐ If worse, restore checkpoint

Jiggle Fitting a Whole Chain

When to use jiggle fitting

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Mar 7, 2026