YARM: Yet Another Relaxation Matrix program
A program for performing nuclear spin relaxation calculations

Sections: Main | Using YARM | Subroutines | Theory | Samples | Resources
Subsections: Introduction
Sample Headers:
Here are a sample headers for YARM scripts.
  • Header structure for YARM scripts.
  • NmrParams Hash structure
  • YarmModel Hash structure
  • Sample Scripts:
    Here are a few useful sample YARM scripts
  • Model validation: analysis of a Model vs NOE data
  • Statistical analysis: entire molecule
  • Statistical analysis: per residue
  • Correlation plot
  • Model refinement: using NOE data to derive a Model
  • Structure refinement
  • Correlation time refinement
  • Intramolecular motion (order parameter) refinement
  • Simple utilities
  • Measuring distances between all protons
  • Measuring a specific distance
  • Measuring angles WRT principal axis
  • Ordering atoms names
  • Sample structures:
    Here are a few PDB files that are used in the sample scripts above.
  • A-form Dickerson dodecamer PDB
  • B-form Dickerson dodecamer PDB
  • XTAL Dickerson dodecamer PDB
  • NMR Dickerson dodecamer PDB