Index

	"CALC"MAP"" Map calculation
.AND.	Operators
.main	Create perl scripts: create_auto_start.pl
.NOT.	Operators
.OR.	Operators
.XOR.	Operators
2FO-FC_MAP	2FO-FC
2FOFC+FOFC	2FOFC+FOFC
3-D images	IMAGE page: displaying of molecular images IMAGE
3angle	3ANGLE Surfaces
3D	IMAGE
academic license	Licenses
ACT_2RES	ACT_2RES
ACT_LAST	ACT_LAST
ACT_NEIG	ACT_NEIG
ACT_SEGM	ACT_SEGM
ACT_SGID	ACT_SGID
ACT_WORK	ACT_WORK
active	CLONE Menu arguments: Selection keys SKEL_IMA SKEL_SYM NICE_SEL Menu arguments: Selection keys Defining 'active' and 'passive' keys
active last	Active last
ADD	ADD
ADD_MODE	ADD_MODE
alpha	SECONDARY Using the secondary structure library
ALT keys	Multiple key shortcuts
amino acids	LIB_PROT
AMoRe	Molecular replacement
analysis	ANALYSIS
ANCHOR	ANCHOR
ANGLE	Force field parameters
angle deviations	ANA_ANGL
ANISO_B	aniso
anisotropic	aniso
anisotropic B-overall	Bulk solvent correction, B-overall anisotropy optimization targets
Anisotropic correction	Anisotropic correction term - bug
argument	Menu arguments: History list Menu arguments: Selection keys Menu arguments: History list Menu arguments: Selection keys Integer number Atom number Real number String
arguments	Using menu items
arrow keys	Arrow keys
asymmetric unit	Score map and skeletons MAP_MASK
atom	RADII BALL BUILD_EXTEND Menu arguments: History list Menu arguments: History list Atom number Atom definition
atom balls	Atom balls
atom conversion	xpl2MAIN MAIN2xpl
atom coordinates	COORDINATES
atom delete	DELE_ATOM
atomic element	Atomic element in the PDB and topology files
atoms	CLONE IMAGE_COL2
atoms history list	HISTORY
atoms to pick	Manipulating the pickable atoms list
ATTACH	ATTACH
auto	AUTO_SEQ
AUTO_FIT	Auto fit button FIT_AUTO
AUTO_SEQ	AUTO_SEQ AUTO_SEQ
AUTO_STUFF	AUTO_STUFF
AUTO_WEI	AUTO_WEI
AUTO_WEIGHT	AUTO_WEIGHT
automated	AUTO_WEI TRACE
automatic	AUTO_SEQ AUTO_STUFF
automation	NEWS: AUTOMATION is ON LINE !!!!!!!
auto scaling	Auto scaling of X-ray, density energy terms versus chemistry terms
auto weighting	AUTO_WEIGHT
averaging	Support of multicrystal averaging DENS_MOD DM_NEXT MAPS page: electron density map calculation Density modification
B-factor	B-VALUES B-VALUES REFINE
B-factor refinement	B-factor refinement
B-value	ANA_TEMP Overall B-value refinement
b-values	TEMPERATURE TEMP_ACT
B-value sharpening	Refining and building at low resolution: B-value sharpening sharp
B_ADD	B-factor refinement
BACK_PDB	BACK_PDB
background	Background images
background color	BACK
ball	BALL
balls	Atom balls Preparing slides
bask	UN_DO
beta	SECONDARY Using the secondary structure library
block	What is a menu block and what an item What is a menu block and what an item
BOND	STICK Force field parameters
bond deviations	ANA_BOND
bonds	Bonds, hydrogen bonds and pair list
bug	Bulk solvent correction term - bug Anisotropic correction term - bug
bugs	Bugs
build	BUILD BUILD_MAIN BUILD_RESI_AUTO MODELER N_MOLECUL
building	BUILD
building unit	Setup of depp pages explained
BULK_SOL	bulk
bulk solvent	Bulk solvent correction term - bug Bulk solvent correction, B-overall anisotropy optimization targets bulk
by chain	Upper line
by segment	Upper line
CALC_BON	CALC_BON
calc_fo_map.cmds	FOBS_MAP
calc_fofc_diff_map.cmds	map FO-FC_MAP
calculate	MAP_DO map FO-FC_MAP FOBS_MAP
calculate map	KICK_STUF Electron density map calculations
calculate maps	CALC_MAP
carbohydrates	LIB_CHO
CCP4 interface	Phase combination
cell.dat	Cell constants file
cell constants file	Cell constants file
center	CENTER CENTER GOTO_SEQ
center list	Center list created from structure validation
chain	CHAIN BUILD CHAIN TRACE RE_ORDER Chain definition
chain memory	Upper line
CHANGE	CHANGE
characters	String
character set	LOAD_FON
clone atoms	CLONE
CNS	Auto start
color	COLOR COLOR IMAGE_COL2 IMAGE_COL Making images of molecules by commands Image object codes and colors
color background	BACK
color definition	Use of color
color index	Use of color
color table	VLT
command	About MAIN, its structure and syntax rules Command sentence Command word
command line	How to start and end a session
communication	User program interactive communication
COMP_SEQ	COMP_SEQ
compare	COMP_SEQ
compatibility	xpl2MAIN MAIN2xpl Topology and parameter files
composition	Setup of depp pages explained
composit models	Reading multiplle PDB files with multiple confirmations
configure	Configure a session by Tk tools "main_config"
conformation	FIX_SIDE RT_CHAIN
conjugated gradients	BY
Connolly	SURFACE IMAGE_DATA
constraints	B-VALUES
contour	Displaying electron density maps
conversion	xpl2MAIN MAIN2xpl Converting XPLOR topology files to MAIN form
coordinates	COORDINATES ATOMS UN_DO COPY_COOR
correction	bulk aniso
covalent bonds	CALC_BON
CRE_OTHER	CRE_OTHER
create_all_others.cmds	Create all related molecules
create_auto_start.pl	Automati detection of NCS from the sequence Auto start Create perl scripts: create_auto_start.pl
create_create_all_others.pl	Create perl scripts: create_create_all_others.pl
create_dm_loop.pl	Create perl scripts: create_dm_loop.pl
create_dm_next.pl	Create perl scripts: create_dm_next.pl
create_dm_prep.pl	Create perl scripts: create_dm_prep.pl
create_gen_solv.pl	Bug fixes Create perl scripts: create_gen_solv.pl
create_load_nmol.pl	Create perl scripts: create_load_nmol.pl
create_main_config.pl	Use of Perl scripts from shell command line Master create perl script: create_main_config.pl
create_make_masks.pl	Create perl scripts: create_make_masks.pl
create_map_calc.pl	CALC_MAP
create_multi_deriv_maps.pl	Create perl scripts: create_multi_deriv_maps.pl
create_phase_comb.pl	PHAS_CMB Create perl scripts: create_phase_comb.pl
create_re_fft.pl	Create perl scripts: create_re_fft.pl
create_re_image.pl	"RE_IMAGE" configuration enhanced Create perl scripts: create_re_image.pl
create_read.pl	Understanding the read.com file Create perl scripts: create_read.pl
create_read.sh	Changing the read.com
create_refine.pl	Create perl scripts: create_refine.pl
create_refine_b.pl	Create perl scripts: create_refine_b.pl
create_restore_file.pl	Create perl scripts: create_restore_file.pl
create_rms_fit.pl	Create perl scripts: create_rms_fit.pl
create_roh_jobs.pl	Create perl scripts: create_roh_jobs.pl
create_rotate_maps.pl	Create perl scripts: create_rotate_maps.pl
create_save_file.pl	Create perl scripts: create_save_file.pl
create_score_map.pl	Create perl scripts: create_score_map.pl
create_scripts	"main_config"
create_symmetry.pl	Create perl scripts: create_symmetry.pl
create_symmetry_ca.pl	Create perl scripts: create_symmetry_ca.pl
create_work_model.pl	Create perl scripts: create_work_model.pl
cross-vector verification	TRANSLATE
crystal data	Crystal forms data
crystal forms	CRYST_NCS Searching in other crystal forms
crystal lattice	SHOW_CEL
CTRL	Multiple key shortcuts
cyclic averaging	DM_NEXT
data	SAVE Understanding the read.com file Saving the current model to disk Reflections
data structures	MAIN data structures
DEF_ALL	Menu arguments: predefined variables Menu arguments: predefined variables
DEF_APPE	DEF_APPE
DEF_DELE	DEF_DELE
DEF_INIT	DEF_INIT
def_top_par_19.com	DEFINE
DEFINE	CENTER DEFINE DEFINE DEPP_MINI Energy calculations and minimization
DEL_ALL	DEFINE
delete	BUILD_EXTEND
delete atom	DELE_ATOM
delete residue	DELE_RESIDUE
denisty modification	MAPS page: electron density map calculation
DENS_MOD	DENS_MOD
density	Auto scaling of X-ray, density energy terms versus chemistry terms Map calculations Displaying electron density maps
density averaging	Use of non-crystallographic similarity (NCS)
density averaging strategy	Changing the averaging strategy
density modification	DENS_MOD DM_NEXT MAP_MASK Density modification Density modification Density modification cycles Density modification loop
density modification initial map	DM_PREP
density target	Density target
deposition	Deposition of MAIN refined files
depp_pages	Origin of the name Depp Pages
depp page	All depp pages menu blocks
depp pages	DEPP pages have two layers Depp pages /Topical pages
depth cueing	CONTRAST
description	Short description of MAIN utilities
deviations	ANA_ENER
diagnosis	Errors and bugs
dialbox	MAIN on LINUX PCs: dials - dialbox 3D graphics window interactions
dialog mode	EXIT
dials	MAIN on LINUX PCs: dials - dialbox 3D graphics window interactions Dials label window DIALS
difference map refinement	Refinement against a difference (Fo-Fc)
difference maps	2FOFC+FOFC
diffract.dat	Diffraction data file
diffraction	Reflections
diffraction data	Diffraction data and formats
DIHEDRAL	RT_CHAIN Force field parameters
direction	SEQ_FORW SEQ_REVE SEQ_BOTH
direct summation	DIRECT
disaster	UN_DO
display	IMAGE Displaying Molecular and Map Images
displaying	Bonds, hydrogen bonds and pair list
displaying maps	MAP
Distances	Distances
dm_loop.com	Density modification loop Density modification loop
DM_NEXT	DM_NEXT
dm_next.cmds	Density modification cycles
DM_PREP	DM_PREP
dm_prep.cmds	Preparation step for density modification cycles
doit	Finish the read.com
duplicate atoms	CLONE
dW	RADII
EACH	Changing the averaging strategy
editing topology	BUILD_EXTEND
elementary	One molecule in an asymmetric unit
end	How to start and end a session
energy	MINIMIZE ANA_ENER Energy calculations and minimization Energy calculations and minimization Force field parameters
energy lists	DEFINE
energy terms	ENERGY
Engh&Huber	LIB_PROT LIB_NU-P
Engh Huber 99	Engh Huber parameters updated to the current version
entry	Create a new entry from atom coordinates
envelope	MAK_MASK MAP_MASK SCOR_MAP Define your asymmetric unit
envelopes	OVERLAP MAP_MASK
error	UN_DO
error recovery	Error recovery and safety
errors	My first trouble shooting Errors and bugs
EXT_SIDE	EXT_SIDE EXT_SIDE
extended	EXT_SIDE
external maps	External maps
fasta sequence	Sequence information data file
fast cooling	Fast cooling versus slow cooling refinement
fcalc	PHASE REFLECTIONS Map calculations
FFT	FOURIER
file	READ
files	SAVE Files
FILL_ATO	FILL_ATO
fill atoms	FILL_ATO
find	WHERE_IS
finish	How to start and end a session
first session	My first MAIN session
fit	RMS_FIT
FIT_PEPT	FIT_PEPT FIT_PEPT
FIT_SIDE	FIT_SIDE FIT_SIDE
fitting	FIT_PEPT FIT_SIDE
FIX_ATOMS	FIX_ATOMS
FIX_PEPT	FIX_PEPT FIX_PEPT
FIX_SIDE	FIX_SIDE FIX_SIDE
flattened	Treatment of solvent region
FLIP_PEP	FLIP_PEP FLIP_PEP
fliping	Flattening and flipping of the solvent region
flipped	Treatment of solvent region
Flip peptide	Flip peptides
flips	FIT_PEPT
FO-FC_MAP	FO-FC_MAP
Fobs	PHASE REFLECTIONS
FOBS_MAP	FOBS_MAP
fonts	LOAD_FON
forces	ENERGY
format	MAP_IO Input data: file, format, geometric parameters Diffraction data file Diffraction data and formats
forward	SEQ_FORW
fourier	FOURIER
free kick maps	FREE KICK refinement
free kick refinement	FREE KICK refinement
Free of charge	Free of charge non-profit use of MAIN
GEN_SKEL	GEN_SKEL
GEN_SOLV	Bug fixes Solvent generation
GEN_SOLVENT	GEN_SOLVENT
general license	Licenses
generate	GEN_SOLVENT
generate surface	POINT
geometry	Moving atoms around
GET_FROM	GET_FROM
get_top_par_19_csd.com	DEFINE
GOTO_ALA	GOTO_ALA
GOTO_HYB	GOTO_HYB
GOTO_SKEL	GOTO_SKEL
goto seqence	GOTO_SEQ
graphic boards	MAIN on LINUX PCs: graphics
graphics	IMAGE Technical data
grasp	GRASP surfaces
grasp surfaces	GRASP surface reading
GUI	Perl Tk config
GUI setup	Configure a session by Tk tools
hardware	Technical data
helices	Using the secondary structure library
helix	SECONDARY
Hendrickson-Latman coeficients	Auxiliary perl scripts: use_mtz.pl
history	Menu arguments: History list Menu arguments: History list
history atoms	HISTORY
hydrogen bonds	Refining and building at low resolution: H-bonds Bonds, hydrogen bonds and pair list Hydrogen bonds
hydrogens	Upper line
ideal values	ANA_ENER
image	Menu arguments: Selection keys IMAGE_DO IMAGE_SEL Menu arguments: Selection keys Displaying electron density maps Displaying Molecular and Map Images Making images of molecules by commands
image center	Command centering
image dialoge	How to start and end a session
image macro	RE_IMAGE
image objects	IMAGE_MENU
image projection	Projection parameters
images	IMAGE Background images
image types	Making images of molecules by commands
IMPROPER	Force field parameters
include	Image object codes and colors
individual	B-VALUES Individual B-value refinement
INITIALIZE	INITIALI
inpud devices	3D graphics window interactions
input	Molecular model data Interfaces to other programs
input.cop	Undo
input diffraction	Diffraction data file
Input file	Input data: file, format, geometric parameters
input sequence	Sequence information data file
INQ_CLAS	INQ_CLAS
inquire	Menu arguments: inquired variables Menu arguments: inquired variables
INSERT	INSERT
integer	Integer number
interaction	User program interactive communication
interactive minimizer	Tethered model building
interfaces	Interfaces to other programs
INV_CHAIN	Invert chain simplified
invert chain	Invert chain simplified
invert chain direction	INV_CHAIN
item	What is a menu block and what an item What is a menu block and what an item
keyboard	3D graphics window interactions Magic of a keyboard touch
keyboard shortcuts enriched	Enriched keyboard shortcuts
key image	Manipulating the pickable atoms list
keys	Menu arguments: Selection keys Magic of a keyboard touch Menu arguments: Selection keys Defining 'active' and 'passive' keys Selections and keys
KICK	KICK DEPP_MINI KICK_STUF KICK_XYZ
KICK_0.3	KICK_0.3
KICK_??	KICK_??
KICK_MAP	KICK_MAP
KICK_SEE	KICK_SEE
kick atoms	KICK
kicked map	KICK_MAP
kicked omit map	OMIT_MAP
kick fcalc	KICK
kicking	Fast cooling versus slow cooling refinement
kick maps	KICK_STUF
kick phases	KICK
kicks	KICKS
l	Start configuration here: Tk_main_config.pl
language	About MAIN, its structure and syntax rules
least-square	Target functions
level	Two levels of user interface
LIB_CHO	LIB_CHO
LIB_NU-P	LIB_NU-P
LIB_PROT	LIB_PROT
library	LIB_PROT LIB_NU-P LIB_CHO Topology and parameter files
licenses	License policy
lights	IMAGE_LIGHT
line	Lines
line thickness	Lines
LINK	Changing the averaging strategy
LINUX	Platform support MAIN on LINUX PCs: graphics MAIN on LINUX PCs: stereo MAIN on LINUX PCs: dials - dialbox
list	CENTER GEN_LIST Menu arguments: History list Menu arguments: History list Force field parameters
load_depp_page.com	Loading menu blocks Loading menu blocks
LOAD_FON	LOAD_FON
LOAD_PDB	LOAD_PDB
load background pdb	BACK_PDB
load menu	Loading menu blocks Loading menu blocks
load pdb	LOAD_PDB
local symmetry	Use of non-crystallographic similarity (NCS) Search for local symmetry within the same crystal form
loops	Building loops
low resolution	Refining and building at low resolution: H-bonds
lwplot	Postscript plot of lines, labels and dots Lwplot
MAC OSX support	Platform support
macros	Macros
magic	Magic of a keyboard touch
MAIN	About MAIN, its structure and syntax rules
MAIN2xpl	MAIN2xpl
main_config	main_config improvements Run main_config first Use of Perl scripts from shell command line "main_config"
MAK_MASK	MAK_MASK
make_masks.cmds	MAK_MASK Molecular envelope creation Molecular envelope creation from atomic model
MAKE_TOP	MAKE_TOP
manual building	BUILD_MAIN BUILD_RESI_AUTO MODELER
map	OVERLAP map FO-FC_MAP FOBS_MAP MAP_MASK SKEL_GEN Map calculations Displaying electron density maps Electron density map calculations
MAP_+_??	MAP_+_??
MAP_2FOFC	Menu arguments: predefined variables Menu arguments: predefined variables
MAP_CALC	MAP_DO
MAP_IO	MAP_DO MAP_IO
map calculation	Map calculation MAPS page: electron density map calculation Map calculations
map correlations	POINTS
map data	Crystal forms data
Map display	Map display
map GUI	CALC_MAP
map images	IMAGE_MAP
map mask	MAP_MASK
map rotation	ROT_MAPS
maps	MAPS MAP_DO Displaying Molecular and Map Images Maps Map INPUT OUTPUT programs and routines
map sticks	Maps
mask	MAK_MASK MAP_MASK SCOR_MAP Density modification loop Define your asymmetric unit
masks	OVERLAP
maximum likelihood	Maximum likelihood has found a way into MAIN Target functions
menu	Depp pages /Topical pages
menu_gen_solv.sh	Solvent generation
menu_read.sh	Changing the read.com
menu block	What is a menu block and what an item What is a menu block and what an item
menu blocks	User menu block communication All depp pages menu blocks
menu item	Multiple key shortcuts What is a menu block and what an item What is a menu block and what an item
menu items	Using menu items Using menu items
merge two residues	MERG_RES
minimization method	BY
MINIMIZE	MINIMIZE Energy calculations and minimization Energy calculations and minimization
minimize energy	DEPP_MINI
minimizer	Improved minimizer
missing atoms	FILL_ATO
mistake	UN_DO
mode	MAIN command line options
model	N_MOLECUL
model bias	KICK_STUF
model rebuilding	Moving atoms around
models	Further steps toward automatization
modification	Density modification cycles
molecular image	IMAGE page: displaying of molecular images IMAGE
molecular mask	MAK_MASK
molecular replacement	Molecular replacement
molecule	IMAGE_DO
molecule creation	CRE_OTHER
molecule rotation	Clear solution(s) found
molecules	Displaying Molecular and Map Images
molecule translation	Clear solution(s) found
mouse	3D graphics window interactions "Depp pages" window Dials label window Mouse usage
MOV_ATOM	MOV_ATOM
MOV_RESI	MOV_RESI
MOV_SELE	MOV_SELE
move residue	MOV_RESI
mrc	MAP_IO
mrc map format	mrc map format support
MTH_ATOM	MTH_ATOM
MTH_AUTO	MTH_AUTO
MTH_TOPO	MTH_TOPO
mtz	Extract information from MTZ files directly Use of Perl scripts from shell command line Phase combination Interfaces to other programs
mtz labels	Auxiliary perl scripts: use_mtz.pl
multicrystal	Support of multicrystal averaging
multiple conformations	Reading multiplle PDB files with multiple confirmations
multiple crystal forms	MACRO
Multiple crystal forms refinement and averaging	Multi crystal forms: refinement and averaging
mutate	CHANGE
N_MOLECUL	N_MOLECUL
name	Origin of the name Depp Pages
NCS	MACRO Applying NCS constraints CRYST_NCS Use of non-crystallographic similarity (NCS) Non-crystallographic symmetry molecular groups
NCS groups	Group inter-dependancy
new topology	Create a new entry from atom coordinates
nmol	Density modification
nmolecules	N_MOLECUL
no graphics	MAIN command line options
non-crystallographic similarity	Applying NCS constraints Use of non-crystallographic similarity (NCS)
nonstandard	Modifying and creating new topology library entries
nucleic acid	LIB_NU-P
number	Integer number Atom number Real number
OB_ACCEPT	Acive objects
OB_REJECT	Acive objects
OB_START	Acive objects
occupancy	WEIGHTS WEIG_ATO REFINE WEIGH_0 WEIGH_1 WEIG_ATO WEIG_SID WEIG_RES WEIG_ACT AUTO_WEI WEIGH_0 WEIGH_1 WEIG_ATO WEIG_RES WEIG_ACT Displaying a molecule and its symmetry mates
OMIT_MAP	OMIT_MAP
omit map	KICK_STUF OMIT_MAP
ONE	Changing the averaging strategy
one letter code	TRP_2_W W_2_TRP
ONL_ANGL	ONL_ANGL
ONL_BOND	ONL_BOND
ONL_CLAS	ONL_CLAS
ONL_DIHE	ONL_DIHE
ONL_IMPR	ONL_IMPR
optimize	MINIMIZE
organize	RE_ORDER
origin	Origin of the name Depp Pages
overall	B-VALUES aniso
overall B	B_ADD
overview	Depp pages /Topical pages
pairs	Bonds, hydrogen bonds and pair list
parameter	LIB_PROT LIB_NU-P LIB_CHO
parameter files	Missing topology and parameter data for residue refinement
parameters	ANA_BOND ANA_ANGL Force field parameters
partial structure factors	bulk
partial structure refinement	MACRO
passive	Menu arguments: Selection keys NICE_SEL Menu arguments: Selection keys Defining 'active' and 'passive' keys
pdb	Deposition of MAIN refined files Auto start Reading multiplle PDB files with multiple confirmations ATOMS Molecular model data Atom coordinate file Interfaces to other programs
peptide	FIX_PEPT FLIP_PEP FIT_PEPT
Perl-Tk	Perl Tk config
Perl scripts	"main_config"
PHAS_CMB	PHAS_CMB
phase_comb.cmds	PHAS_CMB
phase combination	main_config improvements PHAS_CMB Use of phase combination Phase combination
phase extension	Advices for undescribed cases
photo	Preparing slides
picking	Mouse trouble shooting Mouse trouble shooting
picking atoms	HISTORY
pictures	IMAGE Displaying Molecular and Map Images
platform	Technical data
platform supprot	Platform support
plot	PLOT Making plots Lwplot
plots	Making plots
PLOTTER	PLOTTER
points	POINT Points
polygon	3ANGLE
positional	POSITION REFINE REF_ALL
PostScript	Postscript plot of lines, labels and dots
povray	Plots with POVRAY
prepare	DM_PREP
projection	Projection parameters
proper symmetry	Advices for undescribed cases
PURY	Missing topology and parameter data for residue refinement
PUT_TO	PUT_TO
QUIT	How to start and end a session
r-free	PHASE FREE R-VALUES MODUL RANDOM
r-value	PHASE R-VALUES
radii	RADII IMAGE_DATA
radii overlap	OVERLAP
RAMA_PRO	RAMA_PRO
RAMACHAN	RAMACHAN
ramachandran plot	Ramachandran plot RAMACHAN RAMA_PRO
random	KICK_SEE
randomization of atoms	KICK_XYZ
raster3d	Plot command and RASTER3D interface Raster3d plots of sticks, balls, labels and polygonal surfaces
RE_IMAGE	Extended tk_re_image GUI Re_image "RE_IMAGE" configuration enhanced
re_image.cmds	"RE_IMAGE" configuration enhanced Different segments have different colors Displaying a molecule and its symmetry mates
RE_ORDER	Chain reorganization RE_ORDER
re_phase.cmds	Map calculations
RE_SKEL	RE_SKEL
read	READ
read.com	Startup file for N molecules Changing the read.com Understanding the read.com file
READ_ATO	READ_ATO
read atoms	READ_ATO
read map	MAP_IO
real	Real number
real-sapce search	TRANSLATE
real space	POINTS Density target
rebuilding	Moving atoms around
recognize	AUTO_SEQ
recontour	CENTER
REFINE	main_config improvements MINIMIZE REF_ALL
refine.cmds	Refining with NCS Structure refinement
refine_all.cmds	REF_ALL
refine_b.cmds	Refining with NCS Structure refinement
refinement	Refining and building at low resolution: H-bonds Refining and building at low resolution: B-value sharpening Support of multicrystal averaging Maximum likelihood has found a way into MAIN Reciprocal space target function really works now X-TARGET PHASE REFINE REF_ALL Overall B-value refinement Structure refinement Crystallographic refinement Target functions Density target
reflection	REFLECTIONS SELECT
reflections	REFLECTIONS Reflections
remap	CENTER
remove	Image object codes and colors
rename	RENAME RE_ORDER
render.sh	Rendering
render3d	Rendering
renumber	RE_ORDER
reorder	Chain reorganization
RESID ??	RESID ??
residue	BUILD_EXTEND BUILD MAKE_TOP Residue definition Topology and parameter files Modifying and creating new topology library entries Create a new entry from atom coordinates
residue delete	DELE_RESIDUE
residues	Chain reorganization
residues merge	MERG_RES
resolution	Extract information from MTZ files directly REFLECTIONS Resolution
RESTORE	RESTORE
restore file	"REST_FIL" Undo
restraints	B-VALUES
reverse	SEQ_REVE
RGB	COLOR
ribbon	RIBBON RIBBON Ribbons Ribbon
RIG_RESI	RIG_RESI
RIG_SIDE	RIG_SIDE
rigid body	BY
rms	RMS_FIT
RMS_FIT	RMS_FIT
rms_fit.cmds	RMS_FIT Generation of superposition parameters (RMS_FIT)
RMS fit	RMS_FIT
Robert Huber	Robert Huber jobs
RoH_JOBS	RoH_JOBS
RoH jobs	Robert Huber jobs
ROT_MAPS	ROT_MAPS
rotamer	FIX_SIDE
rotamers	Further steps toward automatization
rotate	ROTATE RT_CHAIN RMS_FIT
rotate_maps.cmds	ROT_MAPS Map rotations
rotate and translate	MOV_SELE
rotate chain	RT_CHAIN
rotation	Clear solution(s) found
RT_CHAIN	RT_CHAIN
rules of syntax	Rules of command syntax
safety rules	Error recovery and safety
save	SAVE_AS SAVE Saving the current model to disk
SAVE_AS	SAVE_AS
save_file.cmds	Saving the current model to disk
SAVE_FILE.PDB	Atom coordinate file
SCALE	SCALE
SCALEPACK	Use of Perl scripts from shell command line Diffraction data file Diffraction data and formats
scaleplack	Use scalepack
scattering factors	Atomic element in the PDB and topology files SCATTERI
score map	Score map and skeletons SCOR_MAP
search	POINTS
secondary structure	SECONDARY Using the secondary structure library
seed	KICK_SEE
segment	SEGMENT Segment definition
segment names	Segment Names and their organization
select	Select sequence SELECT SELECT SELECT MAKE_TOP IMAGE_SEL NICE_SEL USE_ATOMS Making images of molecules by commands
selection	Menu arguments: Selection keys Menu arguments: Selection keys Defining 'active' and 'passive' keys Selections and keys
selection keys	Selections and Keys
SELECT OPERATORS	Operators
SELECT TAG SYNTAX	Syntax
seleno methionine	Seleno Methionine residue (SME)
sentence	Command sentence
SEQ_BOTH	SEQ_BOTH
SEQ_FORW	SEQ_FORW
SEQ_REVE	SEQ_REVE
sequence	Select sequence SEQ_FORW SEQ_REVE SEQ_BOTH COMP_SEQ AUTO_SEQ BUILD Molecular model data
sequence root	CHAIN
SET_WEIGHT	SET_WEIGHT
shellx	Diffraction data file
SHELX	Diffraction data and formats
shortcut	Magic of a keyboard touch
shortcuts	Enriched keyboard shortcuts Keyboard shortcuts: magic of a keyboard touch
SHOW_CEL	SHOW_CEL
show WORK_SEGM variable	SHW_SEGM
side chain	Further steps toward automatization FIX_SIDE EXT_SIDE FIT_SIDE
SIGMA_A	Phase combination
sigma a map	Maximum likelihood has found a way into MAIN
sigma cutoff	SIGMA
size	LOAD_FON
sizes	SIZES
SKEL_GEN	SKEL_GEN
SKEL_IMA	SKEL_IMA
SKEL_SYM	SKEL_SYM
skeleton	Skeletonization Score map and skeletons SKEL_GEN Skeletonize your map
skeleton image	SKEL_IMA
skeleton symmetry	SKEL_SYM
slides	Preparing slides
snapshot	Preparing slides
solid maps	IMAGES: Solid maps
solvent	GEN_SOLVENT Solvent generation Treatment of solvent region Flattening and flipping of the solvent region
solvent flattening	SOLV_FLA Density modification
space group	Extract information from MTZ files directly Space group
standard	Topology and parameter files
start	START One molecule in an asymmetric unit "main_config"
starting macro	Understanding the read.com file
step back	UN_DO
stereo	MAIN on LINUX PCs: stereo Stereo in a window under OpenGL STEREO STEREO
stick	STICK
sticks	Sticks Bond sticks Preparing slides
strands	SECONDARY Using the secondary structure library
string	String
structure analysis	ANALYSIS
structure factor	REFLECTIONS
structure factors	PHASE REFLECTIONS Insight into syntax of structure factors manipulation
sugar	LIB_CHO Additional topology (for sugar rings) Additional topology (for sugar rings)
superposition	RMS_FIT RMS_FIT
surface	3ANGLE POINT SURFACE IMAGE_DATA Preparing slides
surfaces	GRASP surfaces Filled surfaces
symmetry	SYMMETRY SYMM_CA COPY_COOR Symmetry operations and cell constants
symmetry.cmds	Different segments have different colors Displaying a molecule and its symmetry mates
symmetry_ca.cmds	Different segments have different colors Displaying a molecule and its symmetry mates
table of colors	VLT
target	Target functions
technical data	Technical data
temperature	TEMPERATURE TEMP_ACT
term	Force field parameters
tether	Energy calculations and minimization
tetherer	Tethered model building
three letter code	TRP_2_W W_2_TRP
tk	Start configuration here: Tk_main_config.pl
tk_config.pl	Perl Tk config
tk_main_config	Automati detection of NCS from the sequence Start configuration here: Tk_main_config.pl
tk_main_config.pl	More GUI-s
tk_re_image.pl	More GUI-s
topical pages	Depp pages /Topical pages
topology	Missing topology and parameter data for residue refinement MAKE_TOP LIB_PROT LIB_NU-P LIB_CHO Changing topology of your model Topology library Topology and parameter files
topology files	Additional topology (for sugar rings) Additional topology (for sugar rings)
topology libary	DEFINE
tracing	TRACE
translate	TRANSLATE RMS_FIT
translation	Clear solution(s) found
TRC_ALA	TRC_ALA
TRC_HYBR	TRC_HYBR
TRC_MERG	TRC_MERG
TRC_ORIG	TRC_ORIG
TRC_SIDE	TRC_SIDE TRC_SIDE
TRC_SKEL	TRC_SKEL
TRC_SYMM	TRC_SYMM
trouble	UN_DO
trouble shooting	Mouse trouble shooting Mouse trouble shooting My first trouble shooting Errors and bugs
TRP_2_W	TRP_2_W
turns	SECONDARY Using the secondary structure library
tutorial	One molecule in an asymmetric unit
un_do	UN_DO
unbiased map	KICK_STUF
undescribed	Advices for undescribed cases
Undo	Undo
unit cell	Extract information from MTZ files directly Symmetry operations and cell constants
unknown	Advices for undescribed cases
update WORK_SEGM variable	UPD_SEGM
urface	Surfaces
USE_ACTI	USE_ACTI
USE_ATOMS	USE_ATOMS
USE_HIST	USE_HIST
use_mtz.pl	Use of Perl scripts from shell command line Diffraction data file Auxiliary perl scripts: use_mtz.pl
use_sca.pl	Use scalepack
USE_WORK	USE_WORK
user interface	Two levels of user interface
utilities	Short description of MAIN utilities
validation	ANALYSIS GEN_LIST
validation list	GEN_LIST
variable	MAIN variables and constants
variables	Menu arguments: inquired variables Menu arguments: predefined variables Menu arguments: inquired variables Menu arguments: predefined variables
variable WORK_SEGM	UPD_SEGM SHW_SEGM
VLT(Video Lookup Table)	VLT
W_2_TRP	W_2_TRP
warnings	My first trouble shooting
WEIG_ACT	WEIG_ACT
WEIG_ATO	WEIG_ATO WEIG_ATO
WEIG_RES	WEIG_RES
WEIG_SID	WEIG_SID
WEIGH_0	WEIGH_0
WEIGH_1	WEIGH_1
weight	WEIG_ATO SET_WEIGHT WEIGH_0 WEIGH_1 WEIG_ATO WEIG_SID WEIG_RES WEIG_ACT AUTO_WEI WEIGH_0 WEIGH_1 WEIG_ATO WEIG_RES WEIG_ACT Displaying a molecule and its symmetry mates
WEIGHTS	WEIGHTS
what	Short description of MAIN utilities
where is	WHERE_IS
WHOLE	Changing the averaging strategy
word	Command word
WORK	WORK
WORK_REFL	Menu arguments: Selection keys Menu arguments: Selection keys
WORK_SEGM	BUILD_EXTEND UPD_SEGM SHW_SEGM Menu arguments: predefined variables DEFINE WORK Menu arguments: predefined variables Understanding the read.com file
write map	MAP_IO
www	Molecular model data
X-PLOR	Auto start Using available X-PLOR topology files
X-ray	Auto scaling of X-ray, density energy terms versus chemistry terms
xpl2MAIN	xpl2MAIN My first trouble shooting
xyz	COORDINATES

Saulius Grazullis is acknowledged for writing the perl script for this keyword index generation.