Concept index for the WHAT IF manual
- %-input
- 2d-graphics
- 3d-database
- 3ssp
- aalten
- access
- a
- 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
- create a gcg msf file
- create cmc file
- create the big file
- dayhof matrix
- delete a profile
- delete profiles
- 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, 3,
- makgcg
- new titles
- profile alignment
- profiles
- read a profile in
- read sequences in
- recovering original sequences
- remove doubble sequences
- 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: 1, 2,
- walcor
- walgra
- write profile file
- write sequence to file
- write sequences out (hssp format)
- allfil
- a
- a
- anealing
- ,
- angles between helices: 1, 2,
- a
- arrow
- a
- ,
- a
- b
- ,
- b
- bugs
- b
- ,
- building in density: 1, 2,
- build
- b
- bumps
- ,
- c-terminal protein extension: 1, 2,
- c
- ,
- centering the screen: 1, 2,
- c
- check
- chi angles
- c
- chi
- c
- ,
- c
- cluster
- c
- colour
- c
- commands
- c
- connolly
- ,
- contact analysis: 1, 2, 3, 4,
- c
- contacts
- contact
- contac
- c
- ,
- contouring a map: 1, 2,
- convex grid points: 1, 2, 3,
- c
- ,
- coordinates listing: 1, 2, 3, 4,
- coordinates
- ,
- correcting residues: 1, 2,
- c
- ,
- c
- d
- ,
- d
- database
- d
- ,
- debumping all residues: 1, 2,
- d
- dgloop
- d
- digitize
- d
- d
- ,
- dna
- d
- drug
- dssp
- e
- electr
- elec
- e
- environment
- essdyn
- e
- e
- family
- f
- flex
- preparing flexx input files: 1, 2,
- f
- g
- ,
- generate database: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
- g
- ,
- g
- ,
- g
- ,
- g
- graphics
- aarrow in allfil
- alpha carbon tracing
- arrow, bend
- arrow, turned
- back bone tracing
- ball and stick models
- ball and stick models of side chains
- ball in allfil
- calpha in allfil
- 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
- fourc in allfil
- hat in allfil
- helix cylinders: 1, 2,
- helix lines
- initialize: 1, 2,
- item in allfil
- linatom in allfil
- line between atoms
- line in allfil
- mollab in allfil
- non molecular objects
- pcklab in allfil
- pckpnt in allfil
- plane in allfil
- plotting items: 1, 2,
- reading dots from a file
- reading lines from a file
- reading whole pictures from a file
- residue in allfil
- 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
- g
- grid
- g
- gromos
- ,
- g
- groups
- ,
- grow protein c-terminal: 1, 2,
- g
- h
- hbonds
- ,
- h
- ,
- help short: 1, 2,
- hidden command listrr: 1, 2,
- hidden options: 1, 2,
- h
- ,
- h
- hssp
- h
- ,
- hydrogen bond parameters: 1, 2,
- h
- hydrogens
- h
- i
- ,
- initialize graphics: 1, 2,
- i
- iris
- items
- j
- k
- l
- labels
- l
- ,
- m
- mapedt
- maps
- map
- m
- masmap
- m
- mdf
- ,
- memory requirements: 1, 2,
- m
- menus
- m
- ,
- molecular dynamics: 1, 2,
- m
- n
- n
- neural
- n
- nmr
- n
- ,
- notebook print: 1, 2,
- notebook write: 1, 2,
- n
- notes
- o
- options
- o
- other
- p
- ,
- parameter setting: 1, 2, 3, 4,
- p
- ,
- p
- parameters
- p
- ,
- phi-psi distributions: 1, 2,
- p
- pir
- p
- plot
- p
- porno
- p
- programming rules
- p
- ,
- p
- ,
- p
- q
- quality
- qualty
- radii
- r
- ,
- ramachandran plot: 1, 2,
- ramachandran plots for database: 1, 2,
- r
- refine
- r
- ,
- renumbering residues: 1, 2,
- r
- ,
- residue contacts: 1, 2, 3,
- r
- residues
- r
- rows
- s
- scan3d inspection
- scan3d
- s
- script
- ,
- secondary structure: 1, 2,
- s
- select
- ,
- self made amino acids: 1, 2,
- s
- ,
- sequence listing: 1, 2,
- sequence patterns: 1, 2,
- s
- shake
- s
- ,
- s
- 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,
- getdsp
- 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
- s
- ,
- structure verification: 1, 2,
- s
- ,
- superposition error: 1, 2,
- suppos
- s
- sym
- t
- ,
- table of accessibilities: 1, 2,
- table of b-factors: 1, 2,
- t
- 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
- make cluster from table
- 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
- t
- ,
- t
- torsion angles
- t
- trajectory
- transformation
- t
- u
- v
- vdw
- ,
- v
- w
- waters
- water
- w
- x
- xray