PHENIX
1. Map Analysis
- phenix.mtriage
- Data Analysis -> Mtriage
2. Map Improvement
- phenix.auto_sharpen
- Map -> AutoSharpen Map, output ccp4 and mtz map files
3. Model Building
- Automatic Model Building
- Model Building > Map to Model, build model from sharpened model and sequence file (fasta)
- Manually Model Building
4. Real Space Refine
- phenix.real_space_refine
- Model that fits the map as well as possible
- Meaningful geometry
- Refinement -> Real-space refinement
- Input files: Model (mmcif), Map (CCP4 .map), Resolution from Data Analysis, Restraint definitions for ligands
- Refinement Settings
- minimazation global
- rigid body
- local grid search
- morphing
- simulated annealing
- adp
- Use secondary structure restrains
- Use NCS
- Restraints
- High to medium resolutions: covalent bond lengths, angles, dihedral angles, planarity and chirality restraints, and a nonbonded repulsion term
- Low resoluiton: secondary structure, NCS
- real_space_refine restraints
- Dsitance and agnle restraints on hydrogen-bond patterns for protein helices and sheets and DNA/RNA base pairs
- Torsion-angle restraints on idealized protein secondary-structure fragments
- Restraints to maintain stacking bases in RNA/DNA parallel
- Ramanchandran plot restraints
- Amino-acid side-chain rotamer-specific restraints
- Cβ deviation restraints
- Reference-model restraints, where a reference model may be a similar structure of better quality or the initial position of the model being refined
- Similarity restraints in torsion or Cartesian space
- NCS constraints
5. Validation
MolProbity
Valdidation -> Comprehensive Validation
- Inputs: Refined Model (pdb or cif), Map file, Resolution
- Outputs: MolProbity Report, or open with Coot
6. Deposition
Reference