Table of Contents for SOLVE on-line manual version 1.17

• Downloading and upgrading SOLVE

• Introduction to SOLVE
  • What SOLVE does
  • Getting Started
    • Scripts
    • Useful commands
    • Running more than one SOLVE job at a time
    • Symmetry files
    • Data files
  • Your license
  • The SOLVEDIR environmental variable
  • Getting more help

• KEYWORD and COMMAND LISTS
  • List of most commonly-used keywords that apply to SOLVE automated operation
  • List of all SOLVE keywords
  • List of all SOLVE commands

• Automated structure determination with SOLVE
  • What you will need to input to SOLVE
  • How to run SOLVE
  • Data formats for automated structure determination with SOLVE
  • Sample scripts for SOLVE
  • How to interpret the solve.status file
  • What to do next after you've run SOLVE
  • How to interpret the output from SOLVE
  • How to export your output from SOLVE to other packages
  • Commands for controlling how SOLVE works in automated mode
  • How SOLVE works
  • Solve examples
    • Gene 5 protein
    • Armadillo repeat of beta-catenin
    • Granulocyte-macrophage colony stimulating factor

• GENERATE: generating and solving model datasets with errors

• SCALING and ANALYSIS OF MIR and MAD data
  • SCALE_MAD: Scaling MAD data
  • ANALYZE_MAD: Analyzing MAD data
  • MADMRG: Converting MAD data to pseudo SIRAS
  • MADBST: Bayesian Fa estimates
  • SCALE_NATIVE: Scaling native data
  • SCALE_MIR: Scaling derivative data
  • ANALYZE_MIR: Analyzing MIR data
  • COMBINE: Combining multiple MAD or MIR datasets
  • HASSP: Searches for solutions to Patterson
  • HEAVY: Heavy atom refinement and phasing

• Local scaling and merging of data
  • Local scaling of data
  • Merging data to the asymmetric unit
  • Completeness of datasets

• DATA formats, and import/export
  • Binary formats used by SOLVE
  • Importing and Exporting data in SOLVE
  • File merging

• Working with maps
  • Calculating maps
  • Peaksearching
  • MAPtoASYM: map a PDB file to asymmetric unit or near an object
  • RHO: electron density at coordinates in a PDB file
  • Omit_map: calculate overlapping omit maps
  • Avg_omit: average overlapping omit maps

• Miscellaneous commands
  • HA_PDB: Write out a heavy atom solution in PDB format
  • COMPARE_SOLN: Comparing two heavy-atom input files
  • MATH: Perform simple operations on datasets
  • GETISO: Get isomorphous differences
  • GETANOM: Get anomalous differences and Fbar
  • GETPHASES: Get phases and F from A, B
  • Weights: weighting for macromolecular refinement
  • Bayesian difference refinement

• New features for version 1.17 of SOLVE

• References for SOLVE

• Copyright statement for SOLVE