Concept index for the WHAT IF manual
- 2d-graphics
- 3d-database
- 3ssp introduction
- 3ssp
- aalten
- ab-initio protein building
- accessibility
- accessibility algorithm
- accessible surface
- access
- adding amino acids
- adding subroutines
- alignment menu introduction
- align
- (re-)set scorings matrix
- add insertion to profile
- aligning profiles
- alignment
- changing the residue type colours
- class identifiers: 1, 2, 3, 4, 5,
- correlated mutations: 1, 2,
- correlation analysis
- correlation file
- corrle
- create a gcg msf file
- create cmc file
- create the big file
- database operations
- dayhof matrix
- delete a profile
- delete sequences
- deleting a sequence
- determine sequence class
- display a sequence
- display alignment
- display scorings matrix
- double sequence checking
- graphical display of sequences
- graphics
- high homology pair search
- how good does sequence fit profile
- interactive graphics
- introduction
- make profile of sequences: 1, 2,
- makgcg
- profile alignment
- profiles
- read a profile in
- read file from swissprot database
- read sequences in
- recovering original sequences
- remove doubble sequences
- scan database
- scoring alignment pairs
- select sequence by keyword: 1, 2,
- seqcol
- sequence directory
- sho profile consensus
- show profile
- skip conserved residues: 1, 2,
- sort by class
- sorting a cmc file
- sorting sequences
- write profile file
- write sequence to file
- write sequences out (hssp format)
- amino acid range(s) i/o
- amino acid regularization
- amino acid, adding of
- anatra
- anchoring chain ends in refinement
- anealing
- angles between helices: 1, 2,
- apply matrix to soup
- applying symmetry to soup
- arrcol
- arrlnp
- arrlns
- arrow
- arrthp
- arrths
- atomic contacts
- atoms colour
- aurelia
- automatic command execution
- average molecules: 1, 2,
- averaging structures
- bailing out: 1, 2,
- ball and stick models
- ball and stick models of side chains
- bugs
- build by adding amino acids
- build protein from scratch
- building from alpha carbons
- building in density: 1, 2,
- build
- bump analysis
- bumps
- c-terminal protein extension: 1, 2,
- canceling options
- cavity search
- cell dimensions
- centering the screen: 1, 2,
- centering the soup
- charges for protein
- checking chain names
- checking torsion angles
- check
- chi angles
- chirality evaluation
- chi
- choose de-activation
- cleaning the soup
- close notebook
- cluster: 1, 2, 3,
- cluster
- colour atoms
- colour menu
- colour ranges
- colour residues
- colour shifting
- colouring mdf reflections
- colour
- command names
- commands executed from a file
- commands from other menu's
- commands
- compare almost identical molecules
- compare equal molecules
- configuration parameters
- connolly: 1, 2,
- connolly execution overview
- connolly inspection of results
- connolly surface
- connolly
- contact analysis: 1, 2, 3,
- contacts of certain atoms
- contacts of certain residues
- contacts
- contact
- contac
- contouring a map: 1, 2,
- convex grid points: 1, 2,
- coordinates list
- coordinates listing
- coordinates
- correcting residues: 1, 2,
- correlation file
- counting contacts: 1, 2,
- cpk model
- creating the database
- cut and paste, undoing
- cys-cys bridge torsion angles
- cys-cys bridges, initialization
- cys-cys bridges, listing
- cys-cys bridges, setting
- cys-cys manipulation
- dashed lines
- data spread sheet: 1, 2,
- database creation
- database inspection
- database
- davadrug
- dayhof matrix
- dayhof scoring matrix
- debumping all residues: 1, 2,
- default map
- delete molecule
- delete molecules
- deleting residues
- depth cueing
- dgloop
- diagonal plot
- diana files
- dimer transformation
- direct action mode
- direct mode
- disk space requirements
- distance geometry
- distribution conditions
- dna fixing: 1, 2,
- dna
- docking
- dot sphere around an atom
- dot surface connolly
- drug design
- drug docking: 1, 2,
- drug
- editing envelops
- electron density convolution
- end notes
- energy minimization
- energy per atom
- energy term plot
- envelop editing
- envelop format
- environment
- environment variables
- essdyn
- extreme coordinates
- family
- fil a gap
- file with commands
- finding options
- fixing alpha carbons in refinement
- fixing atoms in refinement
- fortran pretty printer
- fragment length
- frequently asked questions
- fullstop
- future options
- general notes
- generate database: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
- generate database introduction
- getting started
- grafic menu
- grampp screen menu
- graphics enhancement options
- graphics items: 1, 2,
- graphics menu
- graphics modes
- graphics options
- graphics usage
- graphics
- alpha carbon tracing
- arrow in allfil
- arrow, bend
- arrow, turned
- back bone tracing
- ball and stick models
- ball and stick models of side chains
- center in allfil
- centering the screen: 1, 2,
- circle in allfil
- cluster, showing of
- cone in allfil
- contact analysis
- creating a wire frame cell
- creating multiple wire frame cells
- cross in allfil
- dash in allfil
- display multiple zones
- display whole models
- display whole soup
- dot in allfil
- dot sphere around an atom
- double bonds
- drawing dashed lines
- end in allfil
- hat in allfil
- helix cylinders: 1, 2,
- helix lines
- initialize: 1, 2,
- item in allfil
- line between atoms
- line in allfil
- mollab in allfil
- non molecular objects
- plane in allfil
- plotting items: 1, 2,
- reading dots from a file
- reading lines from a file
- reading whole pictures from a file
- salt bridges
- scale in allfil
- side chain drawing
- sphere in a zone, display
- sphere of residues, display
- stereo mode
- text in allfil
- tricone in allfil
- undisp in direct mode
- wheel in allfil
- grasph
- grid
- gromos output files
- gromos water parameters
- gromos
- group length: 1, 2,
- group statistics
- groups
- grow protein c-terminal: 1, 2,
- grow protein n-terminal
- hand evaluation
- handedness of residues
- hb2net
- hbonds
- helix cylinders: 1, 2,
- helix determination
- helix dipole
- helix lines
- help short: 1, 2,
- hidden command listrr
- hidden commands: 1, 2,
- hidden options: 1, 2,
- history
- history logging: 1, 2,
- hssp file, example
- hssp
- hydrogen bond parameters: 1, 2,
- hydrogen bonds
- hydrogens
- hypertext documentation
- include files
- initialize graphics: 1, 2,
- initializing the soup
- input all
- input total
- inspect database accessibilities
- inspection databse torsion angles.
- installation notes
- installing grid
- interface waters
- introduction to what if
- iris
- items
- known bugs
- labeling atoms
- labels, world view
- labels
- license for what if
- line between atoms
- lines
- logging
- logging results: 1, 2,
- loop searches
- making notes
- map(s), introduction
- mapedt
- maps
- map
- masmap nomenclature
- masmap
- mdf colouring commands
- mdf evaluation
- mdf triggering commands
- mdf
- memory requirements: 1, 2,
- menu params
- menu usage
- menus
- messages.txt
- model building by homology
- mol-items
- mol-objects
- molecular dynamics: 1, 2,
- molecule types
- multi molecule options
- mutant prediction via quality box
- n-terminal protein extension
- nets of water molecules
- neural net
- neural network
- neural
- new notebook
- nmr menu
- nmr options
- nmr
- nomenclature for masmap
- nomenclature of atoms
- notebook
- notebook close
- notebook new
- notebook old
- notebook print: 1, 2,
- notebook write: 1, 2,
- notes for programmers
- notes general
- notes per residue
- notes per residue listing
- notes
- o: original residue name
- objects and items
- old notebook
- operations on rows
- options
- os commands
- other
- overview
- p picking as residue input
- parameter acprec
- parameter correlation rows
- parameter setting: 1, 2, 3, 4,
- parameter values
- parameters: 1, 2,
- parameters (internal)
- parameters for build menu
- parameters for scan3d
- parameters for tables
- parameters for water menu
- parameters
- params (hydrogen bonds)
- params.fig
- percent input
- percent sign
- percent symbol
- perspective
- pick options help
- picking atoms
- pir files
- pir
- place helices
- plot options
- plot parameters
- plot
- porno
- pqms.exe
- predefined ranges
- prediction of mutants
- pregromos what if version
- print notebook
- privat menu
- probes for grid
- profiles
- program parameters: 1, 2, 3,
- programming rules
- programming rules
- protein charges
- protein folding
- protons: 1, 2,
- pull down menus: 1, 2,
- pulldown menus
- quality box mutant prediction
- quality control
- quality control boxes
- quality paramers
- quality parameters
- quality
- qualty
- radii
- radius
- radius of rolling sphere
- ramachandran plots for database: 1, 2,
- randomizing coordinates
- real space refinement
- recalling options
- refinement
- refine
- refinment parameters: 1, 2,
- regularisation
- relational database
- relational database, usage of
- release of next version
- renaming commands
- renumbering residues: 1, 2,
- repairing the soup
- repeating options
- residue contacts: 1, 2, 3,
- residue numbers
- residue range(s) i/o
- residues colour
- residues near a water
- residues restoring
- residues
- restoring rows
- result logging
- retrieving all rows
- retrieving one row
- ribbons
- rotamer normality
- rotating a molecule
- rows write row in table
- rows
- s input
- save view matrix
- saving all rows
- saving one row
- saving rows
- scan database backbone hbonds
- scan database for accessibilities
- scan database for atomic contacts
- scan database for chi-angles
- scan database for conservation
- scan database for helix, sheet
- scan database for hydrophobic moments
- scan database for omega
- scan database for phi, psi
- scan database for turn types
- scan database related sequences
- scan sequences
- scan3d inspection
- scan3d inspection
- scan3d
- scanning the relational database
- scoring matrix, dayhoff
- screen dump
- script repetition
- script
- secondary structure: 1, 2, 3,
- selecting predefined ranges
- select
- self made amino acids: 1, 2,
- sequence alignment
- sequence database operations
- sequence files
- sequence listing
- sequence manipulations
- sequence patterns
- set cell dimensions
- set name
- setvdw menu
- sheet determination
- shifting colours
- shohst initialize
- shopar (hydrogen bonds)
- short help: 1, 2,
- show groups of waters
- show quality parameters
- simulated anealing
- solid surface by connolly
- soup hidden options
- soup paste everything
- soup set name
- soup
- (re-)centering
- bad residues
- chain-identifiers, changing or setting
- changing or setting chain-identifiers
- contents
- copying part of the soup
- correct all residues
- correct residues
- cut, undoing
- cys-cys bridges
- cys-cys bridges, setting
- cys-cys initialization
- cys-cys listing
- delete molecule
- delete molecules
- deleting base pairs
- fixing dna: 1, 2,
- initializing the soup
- introduction
- list contents
- merging drugs
- molecule types
- paste, undoing
- re-centering
- renumbering residues
- repair
- restoring residues: 1, 2,
- saving residues: 1, 2,
- show cut and paste flags
- sousph
- spacegroups
- spawning a subprocess
- spline
- spread sheet
- sql (not used)
- startup script
- steve gardner
- stick
- subprocess spawning
- subroutine addition
- superimposing structures
- superposition
- superposition error: 1, 2,
- suppos
- surface accessibility
- surface area analysis
- surface by connolly lines
- surface by connolly triangles
- surface rendering
- symmetry contacts
- symmetry parameters
- symmetry related objects: 1, 2,
- symmetry transformed graphics objects
- sym
- table combination
- table of accessibilities: 1, 2,
- table of b-factors: 1, 2,
- table of energy terms
- table of hydrogen bonds
- table of property values
- table of real space density
- table of residue names
- table of residue quality
- table of residue types
- table of secondary structure
- table of sequence
- table of symmetry contacts
- table of torsion angles
- table with numbers
- tables parameters
- tables
- accessibility table: 1, 2,
- adding tables
- angular difference between tables
- average of two tables
- b-factor table: 1, 2,
- combining
- correlation with residue types
- create logical table: 1, 2, 3,
- creation of
- creation of tables
- deleting
- deleting tables
- difference statistics
- display table
- display values at graphics
- energy term table
- formatted table file
- h-bond table
- initialization
- introduction
- introduction. general.
- invert a logical table
- list of tables
- listing
- listing them
- logical and
- logical or
- logical statistics per residue type
- mark difference between two tables: 1, 2,
- maximum of two tables
- minimum of two tables
- multiplying tables
- parameters
- plot table
- property value table
- real space density table
- residue name table
- residue quality table
- residue type table
- restoring tables
- saving tables
- scatter plot
- secondary structure table
- sequence table
- shifting: 1, 2,
- shifting up and down: 1, 2,
- subtracting tables
- symmetry contact table
- table to property
- table with numbers
- tabulate bumps
- torsion angle table
- write table in file
- writing to file
- teaching module
- terminal i/o
- thornton
- topology file: 1, 2, 3,
- torsion angle evaluation
- torsion angle manipulation
- torsion angles of cys-cys bridge
- torsion angles
- trajectory analysis
- trajectory graphics
- trajectory
- transformation
- translating a molecule
- trb.exe
- triggering mdf reflections
- turn determination
- tutorial
- two dimensional graphics
- type ahead
- u input
- undoing anchoring chain ends
- undoing fixing atoms in refinement
- usage of graphics
- user i/o
- user interaction
- user written subroutines
- using the database
- vacacc
- van der waals radii: 1, 2,
- van der waals radii, default
- van der waals surfaces
- vanderwaals surface
- vdw
- version level: 1, 2,
- vet file
- view matrix restoration
- view matrix, saving of
- view matrix, use of external
- view optimalisation
- waals
- water parameters
- water potential positions
- water statistics
- waters near one residue
- waters near residues
- waters
- water
- what if
- what if 5.0
- what if intro
- what if possibilities
- what if, introduction
- what if, why this name
- why the name "what if"
- wilson plot
- working model removal
- write notebook
- writeup
- x-ray menu
- x11 configuration
- xray menus
- xray menus, introduction
- xray