# Table of Contents for SOLVE on-line manual version 2.13

SOLVE Alphabetical Index#### SOLVE FAQS page

#### Introduction to SOLVE

#### Your license

#### The SOLVEDIR, SOLVETMPDIR, and CCP4_OPEN environmental variables

#### 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

#### 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

#### DATA formats, and import/export

#### 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
- CART_TO_FRACT and FRACT_TO_CART: conversion from fractional to cartesian coordinates

#### New features for versions 1.18/1.19/2.01/2.02/2.03/2.04/2.05/2.06/2.08/2.09/2.10 of SOLVE/RESOLVE

#### References for SOLVE

#### Copyright statement for SOLVE