Contents
Release 2005, March 2005
1. Introduction
- NMR structure determination
- NMR data processing and analysis
- Hardware recommendations
- Installation
- How to invoke NMRchitect
- Note on command names
- Operations
2. Theory
- Overview of data processing and spectral analysis
- Overview of restraint generation
- Distance geometry
- Describing molecular conformation
- Covalent distance constraints
- Vicinal distance constraints
- Chirality constraints in distance geometry
- Constraining torsion angles
- Steric distance constraints
- Conformational distance constraints
- Bound smoothing
- Triangle bound smoothing
- Tetrangle inequality bound smoothing
- Embedding coordinates from distances
- Metrization
- Embedding
- Majorization
- Optimization of the coordinates
- Error function
- Simulated annealing associated with DGII
- Minimization and analysis
- Calculation of theoretical nuclear overhauser effects (NOE's)
- Multi-spin relaxation
- Direct NOE refinement
- Introduction
- Efficient calculation of NOE's
- Calculation of the gradients
- Methyl group and ring flipping
- Simulated annealing using a physical forcefield
- Target function
- Covalent structure
- Nonbond form
- Conformational distance and dihedral restraints
- NOE volume restraints
- 3J dihedral restraints
- Chirality restraints
- NOE overlapped distance restraints
- NOE overlapped volume restraints
- Simulated annealing calculation
- Starting conformation
- Scaling methods
- Preparation
- Sampling
- Folding
- Regularization
- Cooling
- Minimization
- Rattle
- Summary
- Iterative relaxation matrix approach
- Overview of IRMA
- R-factors
- Solvent accessible surfaces
- Definition of solvent accessible surface area
- Significance of solvent accessible surface area
- Solvation module versus ProStat
- Solvent accessible surface area for protein structure validation
- Rules for protein validation
3. Implementation
- Module architecture
- Felix
- NMR database
- Introduction
- NMR project tracking
- Restraints and the NMR molecule
- Description of NMR database files
- .ppm file
- .asn file
- .pks file
- .rstrnt file
- File version incrementing
- NMRchitect naming conventions
- Pseudoatom definitions and labels
- Prochiral labeling
- Restraint subset definitions
- Automatic error checking of the NMR data
- Distance geometry
- Database files
- Treatment of chirality and prochirality in DG II
- Step 1 programs and files
- Step 2 programs and files
- Step 3 programs and files
- Support programs
- Simulated annealing using a physical forcefield
- Application of simulated annealing to polypeptides
- Simulated annealing protocol
- Database consistency
- Data flow
- Temperature control within simulated annealing
- Using tables to assist in protocol development
- NOE volume information as input into Discover
- Peak classes and treatments
- Reference peaks
- Cutoff distance
- Derivative cutoff
- Scaling
- Imposing distance limits per volume restraints
- Reducing the force due to redundant distance restraints
- Updating criterion
- Executing the calculation
- Simulated annealing output generated by Discover
- Computational limits for NOE refinement
- Overlapped distance
- Limits on overlapped peaks
- Overlapped volume
- Imposing distance limits per volume restraints
- Reducing the force due to redundant distance restraints
- Limits on overlapped peaks
- Iterative relaxation matrix approach
- RMA scheme
- Ensemble averaging
- Generation of theoretical and experimental NOE matrices
- Back-transformation and distance refinement
- IRMA files
- Using pseudoatoms with IRMA
- CH3 motional averaging
- No averaging
- 1/r6
- 1/r3
- Ring motional averaging
- No averaging
- 1/r6
- Equivalent peaks
- Pseudoatoms not treated by RMA
- Iteration and convergence
- R-factors
- Relaxation matrix approach data structure
- Input files for RMA background job
- Output files
- Insight II interface to IRMA
- IRMA interface to distance geometry (DGII)
- IRMA interface to simulated annealing (MD_Schedule)
- IRMA interface to Felix
- Computational limits
- Debugging an RMA run
- Structure determination using X-PLOR
- X-PLOR format restraint files
- Reading and writing restraints
- Job control
- PDBX_File_Name
- Use_Assembly
- PSF_File_Name
- Param_File_Name
- DGSA: distance geometry and simulated annealing
- Energy minimization
- SA_Refine: simulated annealing refinement
- Restrained molecular dynamics
- TAD: torsion angle dynamics
- Custom: customized restrained molecular dynamics
- Preview of customized X-PLOR scripts
- ARIA
- Introduction
- Using Aria
- Input Data
- Overview of ARIA options
- NMR analysis tools
- Restraint subsets
- Reading, writing, and deleting restraint subsets
- Displaying restraint subsets
- Coloring restraint subsets
- Graphing restraint subsets
- Editing restraints
- Chiral restraints
- Dihedral restraints
- Distance restraints
- 3J restraints
- Manipulating restraints by class
- Structural and dynamics analysis using Query
- Table creation
- Table promotion
- NMR property calculation
- Distance_Avg
- Order_Parameters
- XYZ_RMSD
- Proton_NOE
- ProStat--Protein structure analyst
- Structure checking
- Residue dihedral angles
- Secondary structure classification
- Algorithmic implementation
- United atom models
- Setting atomic radii
- Definition of computed surface areas and their significance
- Total surface area
- Relative surface area and the tripeptide model
- Polar and apolar surface area
- Limitations in implementation
4. Command Summary
- NMR_DB pulldown
- NMR_DB/Files
- NMR_DB/Restraints
- NMR_DB/Subsets
- NMR_DB/Pseudo_Corrections
- NMR_DB/Stereo_Assign
- NMR_DB/Edit_PPM
- Pseudo_Atom pulldown
- Distance pulldown
- Distance/Display
- Distance/Color
- Distance/Label
- Distance/Graph
- Distance/Statistics
- Distance/Edit
- Distance/Edit
- Distance/List
- Dihedral pulldown
- Dihedral/Display
- Dihedral/Color
- Dihedral/Label
- Dihedral/Graph
- Dihedral/Statistics
- Dihedral/3J_To_Dihed
- Dihedral/List
- Chiral pulldown
- Chiral/Color
- Chiral/Label
- Chiral/List
- NOE_Volume pulldown
- NOE_Volume/NOE_Simulate
- NOE_Volume/Graph_Buildup
- NOE_Volume/Display
- NOE_Volume/Color
- NOE_Volume/Label
- NOE_Volume/Statistics
- NOE_Volume/Edit
- Query pulldown
- Query/Table_Create
- Query/Table_Promote
- Query/Distance_Avg
- Query/Order_Parameters
- Query/XYZ_Overlap
- Query/XYZ_RMSD
- Query/Proton_NOE
- Query/Chemical Shift
- Query/Color_By_SAR
- IRMA pulldown
- IRMA/RMA_Run
- DGII pulldown
- DGII/DGII_Params
- DGII/DGII_Run
- DGII/DGII_Tabulate
- DGII/DGII_Analysis
- MD_Schedule pulldown
- MD_Schedule/Get
- MD_Schedule/Put
- MD_Schedule/Edit
- MD_Schedule/Run
- MD_Schedule/MD_Analysis
- XPLOR pulldown
- XPLOR/Setup
- XPLOR/DGSA
- XPLOR/Minimize
- XPLOR/SA_Refine
- XPLOR/Dynamics
- XPLOR/TAD
- XPLOR/Custom
- XPLOR/Preview
- XPLOR/ARIA
- XPLOR/XPLOR_Analysis
- XPLOR/GetPDBEnsemble
- Job_Control
- Rstrnt
- Protocol
- Iteration
- Run
- XPLOR/XPLOR_Analysis
- ProStat pulldown
- ProStat/Struct_Check
- ProStat/Residue_Dihedral
- ProStat/SecondaryClassify
- ProStat/Access_Surf
- Background_Job pulldown
- Felix pulldown
- Felix/Start_Felix
- Felix/Write_To_Felix
- Felix/Read_From_Felix
- Felix/Command
- Felix/Find_Peak
5. Methodology
- Felix
- DGII
- Bounds generation and smoothing
- Metrization and embedding
- Optimization
- Simulated annealing
- Schedule
- Starting structure
- Preparation
- Folding
- Cooling
- Minimization
- Rattle
- Restraints
- Peptide bond planarity
- Using 3J dihedral restraints
- Summary
- 3J Dihedral methods and parameters
- IRMA
- Refinement and restraint generation using IRMA
- Guidelines for a general IRMA strategy
- Effects of starting structure, correlation time, and scaling methods on IRMA distance restraints
- Starting structure
- Merged intensity matrices
- Physical parameters in IRMA
- Correlation Time
- Diagonal Leakage Rate
- Reference peaks
- Distance bounds
- R-factors
- Viewing NOE buildup data
- Visualizing theoretical NOE spectra
6. Tutorials
- Overview of tutorial lessons
- Pilot online tutorials
- Tutorial lessons in this chapter
- Preparing to run the lessons in this chapter
- Macros
- Lesson 6: Using DGII for a cyclic peptide with a nonstandard backbone and side chains: cyclosporin A
- Lesson 9: IRMA theoretical NOE intensity calculation
- Lesson 13: Felix interface
A. References
B. Glossary
C. File Formats
- Introduction
- Global Identifiers
- Labeling Conventions
- Insight II Files
- .asn (Peak Assignment) File Format
- .asn File Example
- .rsub (Restraint Subset) File
- .rsub File Format
- .rsub File Example
- IRMA Files
- .shift File Format
- .shift File Example
- .mdh File Format
- .mdh File Example
- .rmainp File Format
- .rmainp File Example
- .rma (Relaxation Matrix Parameters) File Format
- .rma File Example
- X-PLOR Files
- .xdcn (XPLOR NOE Distance Restraints) File Format
- .xdih (XPLOR Dihedral Restraint) File Format
- .xint (XPLOR NOE Volume Restraint) File Format
Figures
- 1. Biomacromolecular structure elucidation based on multi-dimensional NMR spectroscopic data
- 2. Tetrangle inequality limits
- 3. Diagram of the scaling of force constants in simulated annealing
- 4. Schematic presentation of the IRMA procedure
- 5. Overview of DGII
- 6. DGII bounds generation and smoothing data flow
- 7. DGII metrization and embedding data flow
- 8. DGII optimization data flow
- 9. Data flow for a simulated annealing schedule using a physical forcefield
- 10. IRMA schematic
- 11. Building the NOE matrices
- 12. Extracting the refined distances from the merged NOE matrix
- 13. Data flow for structure generation and refinement using X-PLOR
- 14, X-PLOR custom script preview
- 15. Simulated annealing methodology
- 16. IRMA strategy for iterative refinement of a family of conformers
- 17. IRMA strategy for iterative refinement of a single conformer
Tables
- 1. Some standard A, B, C coefficients
- 2. RMS difference (Å) between simulated annealing and X-ray structures
- 3. Pairwise RMSD for SA-6 crambin structures in Å*
- 4. Parameters for torsion angles
- 5. Shrake & Rupley (1973) united atom model
- 6. Lee and Richards (1971) united atom model
- 7. RMS deviations in IRMA refined distance restraints
-
Last updated May 23, 2001.
Copyright © 2001, Accelrys, Inc. All rights
reserved.