Table of Contents for SOLVE on-line manual version 2.13

SOLVE Alphabetical Index

SOLVE FAQS page

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, 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

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
• 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