Turbo-Frodo

User's Manual

Version 5.5

Table of Contents

Introduction

PART I

PART II

Chapter 3: Textport Orders: Main Commands to Manage the Files
- DELETE
- FREAD
- LIST
- LOAD
- MAKE
- RAD
- READ
- SELECT
- UNLOAD
Chapter 4: Textport Options: 48 Options to Parameterize and Display

PART III

Chapter 7: The Color Menu: Coloring the Molecule
- SAME
- ATOM TYPE
- RESIDUE TYPE
- SIDE CHAIN
- FEATURE (submenu)
- B-FACTORS
- SECOND STRUCT
- ACCESSIBILITY
- HYDROPATHY
- DEFINE (submenu)
- ATOM TYPE DEF
- RES TYPE DEF
- SECOND STRUC
- B-FACT RANGE
- HYDR RANGE
- ACCESS RANGE
- DIST COLOR
- SAVE DEFINE

Chapter 9: The Editing Menu: Editing the Structure
- DELETE
- INSERT
- REPLACE
- SHEET/HELIX
- ADD ATOM
- [WAT]/CA
- DEL ATOM
- OPEN MODEL (submenu)
- OPEN MODEL
- CONSTRUCT (sub-submenu)
- ADD FRAG
- ADD ATOM H
- REPLACE ATOM
- DEFINE RESIDUE
- DEFINE ANGLE
- DEFINE DIST
- DEFINE ATOM
- DATA BANK (submenu)
- SEARCH NAME
- SEARCH CHEMIC
- USER DICT
- CONNECT-MOLECULE

Chapter 10: The Modeling Menu: Designing the Molecule
- BOND
- BREAK BOND
- FRAG ROT/TRANS
- MOVE ATOM
- REFINE
- DGNL
- DGNL PICK
- TORSION (submenu)
- TORSION-PICK
- TORSION-AUTO
- DENS-SEARCH
- DIST-SEARCH
- RSR-WAT
- RSR-FULL

Chapter 11: The View Menu: Representing the Structure.
- SPHERE
- CA
- BACKBONE
- CA-SIDE-RES
- CA-SIDE-NAME
- NO HYDROGEN
- SMALL CIRCLE
- LABEL ATOM (submenu)
- LABEL TYPE
- DEF FONT
- COLOR LABEL
- COMPACT SELE (submenu)
- CPK
- BALL & STICKS
- COMPACT ROT
- CURVE LINE
- CURVE PATCH
- STRUC REP
- STRUC MENU
- RESET STR MENU
- COMPACT-DO-IT
- MAP SPHERE

Chapter 12: The Plot Menu: Graphs and Postscripts
- WRITE MATRIX
- GRAPHICS (submenu)
- GRAPH B-F ALL
- GRAPH B-F M/S
- DIFF B-F ALL
- DIF B-F M/S
- GRAPH
- RAMA ALL
- ALL MODE
- SEQUENCE
- SET VIEW (submenu)
- PLOT
- PLOT FRAME
- TITLE
- PHOTO
- SCREENSAVE
- SCREENSAVE ALL
- WHITE BACK

Chapter 13: The Tools Menu: The Workshop
- RIGID 2
- SCAN
- MAPS (submenu)
- MAPS
- BUILDING (submenu)
- MAKE FRAGS
- HIDE FRAGS
- ALIGN FRAGS
- ADD TPPR
- MULTI REPLACE
- TOOLS BOX (sub-submenu)
- RESI ROT/TRANS
- RSR MAIN
- RSR SIDE
- ROTAMERS
- CA LABELS
- BONES (submenu)
- Bones Labels
- BONES ON/OFF
- 8 CELLS
- BONES MAIN
- BONES SIDE
- UNDEFINED
- BONES SAVE
- BONES C ALPHA
- CREATE CA
- CREATE TPPR
- SYMMETRY (submenu)
- SYM NEIGH
- 1 CELL
- 27 CELLS
- 1 BOX
- 27 BOXES
- CELL CONTENT
- DEL SYM
- NO SYMM
- NCS (submenu)
- APPLY MATRIX
- AUTO APPLY
- NCS MAPS
- PRINT NCS
- NMR (submenu)
- NMR ON/OFF
- VIOLATIONS
- COL REST ATO
- COL REST RES
- DISPLAY RES
- PSEUDO-HYDS
- NO PSEUDOS
- TRAJECTORY (submenu)
- DEFINITION
- STATIC
- DYNAMIC
- SECOND STRUCT (submenu)
- HELIX, SHEET, TURN, COIL
- FAST CALC
- DSSP CALC
- ACCESS CALC

PART IV