For NMR Spectroscopists

Note for Spectroscopists

If you are coming from an NMR background (XPLOR-NIH, CYANA, CNS):

• Structure Calculation vs. Generation: synth-pdb mimics the final stage of an NMR structure calculation: Geometry Regularization (minimization in implicit solvent).
• Proton Detection: Unlike X-ray, NMR relies on 1H spins. That's why we explicitly add hydrogens before minimization.

Synthetic NMR Data

NOE Restraints (--gen-nef)

Generates distance restraints based on geometric proximity. - Criteria: H-H distance < cutoff (default 5.0 Å) - Format: NMR Exchange Format (NEF)

Chemical Shifts (--gen-shifts)

Generates predicted chemical shifts (\(\delta\)) using SPARTA-lite: - Helix: \(C_\alpha\) +3.1 ppm - Sheet: \(C_\alpha\) -1.5 ppm

Relaxation Data (--gen-relax)

Simulates \(R_1\), \(R_2\), and NOE based on Model-Free formalism. - Order Parameter (\(S^2\)): Derived from local flexibility. - Tumbling Time (\(\tau_c\)): Configurable via --tumbling-time.