Index

"CALC"MAP"" Map calculation
"refine.cmds" Configure "refine.cmds"
"create_refine.pl" Configure "refine.cmds"
.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
average of KICK_??
averaging Support of multicrystal averaging
DENS_MOD
DM_NEXT
MAPS page: electron density map calculation
Density modification
b-factor B-VALUES
B-VALUES
REFINE
REF_B
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
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
CALC_BON CALC_BON
calc_fo_map.cmds FOBS_MAP
calc_fofc_diff_map.cmds 2FO-FC
FO-FC_MAP
calculate MAP_CALC
2FO-FC
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
CHANGE CHANGE
characters String
character set LOAD_FON
chirality INV_CHIR
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
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 "main_config"
conformation FIX_SIDE
RT_CHAIN
conjugated gradients BY
CONNECT CONNECT
Connolly SURFACE
IMAGE_DATA
constraints B-VALUES
contour Displaying electron density maps
conversion xpl2MAIN
MAIN2xpl
Converting XPLOR topology files to MAIN form
cooling Positional refinement
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 Run main_config first
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 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 end
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 Positional refinement
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 end
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
RT_BETWE
FO-FC_MAP FO-FC_MAP
Fobs PHASE
REFLECTIONS
FOBS_MAP FOBS_MAP
fonts LOAD_FON
forces ENERGY
format 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
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
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 end
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
REF_B
Individual B-value refinement
INITIALIZE INITIALI
inpud devices 3D graphics window interactions
input Interfaces to other programs
input.cop Undo
input diffraction Diffraction data file
Input files Input data: files and 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
interfaces Interfaces to other programs
INV_CHAIN Invert chain simplified
INV_CHIR INV_CHIR
inverse INV_CHIR
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_SEED
KICK_XYZ
KICK_0.3 KICK_0.3
KICK_0.3
KICK_?? KICK_??
KICK_??
KICK_MAP KICK_MAP
KICK_MAP
KICK_SEE KICK_SEE
KICK_SEED KICK_SEED
kick atoms KICK
kicked map KICK_MAP
kicked omit map OMIT_MAP
kick fcalc KICK
kicking Fast cooling versus slow cooling refinement
kick map KICK_0.3
KICK_??
kick maps KICK_STUF
kick phases KICK
kicks KICKS
kick seed KICK_SEED
l 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
Run main_config first
"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
map OVERLAP
2FO-FC
FO-FC_MAP
FOBS_MAP
target
MAP_MASK
SKEL_GEN
Map calculations
Displaying electron density maps
Electron density map calculations
MAP_+_?? MAP_+_??
MAP_+_??
MAP_2FOFC Menu arguments: predefined variables
Menu arguments: predefined variables
MAP_CALC MAP_CALC
map calculation Map calculation
MAPS page: electron density map calculation
Map calculations
map correlations POINTS
Map display Map display
map GUI CALC_MAP
map images IMAGE_MAP
map mask MAP_MASK
map rotation ROT_MAPS
maps MAPS
MAP_CALC
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
maximum likelyhood target
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
ML map target
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_DIST MOV_DIST
MOV_RESI MOV_RESI
MOV_RT_6 MOV_RT_6
MOV_SELE MOV_SELE
move residue MOV_RESI
MTH_ATOM MTH_ATOM
MTH_AUTO MTH_AUTO
MTH_TOPO MTH_TOPO
mtz Extract information from MTZ files directly
Run main_config first
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)
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
omit map KICK_STUF
OMIT_MAP
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
REF_B
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
Atom coordinate file
Interfaces to other programs
peptide FIX_PEPT
FLIP_PEP
FIT_PEPT
RT_BETWE
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_XYZ
Positional refinement
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 end
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 RT_BETWE
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
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_XYZ
refine.cmds REF_XYZ
Positional refinement
Refining with NCS
Structure refinement
REFINE_B REF_B
refine_b.cmds REF_B
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_XYZ
REF_B
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
ROTATE
RT_CHAIN
RMS_FIT
rotate_maps.cmds ROT_MAPS
Map rotations
rotate and translate MOV_SELE
rotate atoms RT_BETWE
rotate chain RT_CHAIN
rotation Clear solution(s) found
RT_ANGLE RT_ANGLE
RT_BETWE RT_BETWE
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 Run main_config first
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
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
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 target
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
three letter code TRP_2_W
W_2_TRP
tk tk_main_config.pl
tk_config.pl Perl Tk config
tk_main_config Automati detection of NCS from the sequence
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
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
UN map target
update WORK_SEGM variable UPD_SEGM
urface Surfaces
USE_ACTI USE_ACTI
USE_ATOMS USE_ATOMS
USE_HIST USE_HIST
use_mtz.pl Run main_config first
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
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.