Insight II


Index

A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z



A

ACE
Inhibitor Captopril 133
pharmacophore model 151
Activity_Prediction command
Module pulldown 66
Adams, N. 307
Add command
Assembly pulldown 96
Add_To_Pulldown command
Custom pulldown 101
Aldehyde 138
fragment 138
Alias command
Session pulldown 74
AM_Analyze pulldown
commands in 178
AM_Parameters pulldown
commands in 177
AM_Run pulldown
commands in 178
AM_Setup pulldown
commands in 175
amide
bond 138, 147, 152, 156
Ampac/Mopac 6
Ampac/Mopac command
Module pulldown 68
Ampac/Mopac module 17
tutorial 181
Analysis 5
Analysis command
Module pulldown 69
Analysis module 17
tutorial 205
Angiotensin Converting Enzyme (ACE) 133
Angle command
Measure pulldown 87
Angle_Def command
Trajectory pulldown 202
Animate command
Trajectory pulldown 195, 200
memory limitations 205
methodology 205
Annotate command
User pulldown 99
Apply command
Transform pulldown 92
aromaticity test 340
assembly
equivalent to family 201
Assembly pulldown 66
commands in 96
Assimilate 138
Associate command
Assembly pulldown 96
Atom pulldown
commands in 113
in Builder module 113
atom tests 339
auto-correlations 210
average plane evaluation 191
Axes command
Transform pulldown 90
Axes_Display command
Object pulldown 79
Axis_Function command
Trajectory pulldown 201
methodology 204

B

background color 71
background job
completion status 220
default mode 219
execution mode 220
host 220
requirements for running on a remote host 217
Background_Job
application 218
command summary 218
commands in 178, 203, 218
methodology 219
Background_Job pulldown
commands in 178, 203
in Analysis module 199
Background_Job tutorial
using the Ampac/Mopac module 221
Baker, J. 163, 164, 307
Banerjee, A. 164, 307
Bergeron, D. 164, 307
Biopolymer command
Module pulldown 66
Biopolymer module 17
Biosym Command Language
see also BCL 223
with Custom pulldown 100
Blank command
Object pulldown 79
Blink command
Object pulldown 79
Bond_Order command
Molecule pulldown 84
Boolean command
Graph pulldown 211
Bracewell
reference 194
Brookhaven
Protein Data Bank 2
Brookhaven database
molecule from 38
Browse command
Molecule pulldown 85
Buffer command
Session pulldown 74
Builder 2, 4, 134, 136, 145, 151
Builder command
Module pulldown 66
Builder module 17
Builder module 133
Builder tutorial 130
bulk density 198, 199
Bump command
Measure pulldown 88
Button command
Session pulldown 75

C

Calculation command
AM_Setup pulldown 176
Cambridge
data files 2
Cambridge Crystal database
molecule from 38
Captopril 134, 135, 149
Using Sketch 145
carboxyl
group 134, 147, 148, 152, 153, 156
oxygen 152
case sensitivity 76
Catalogue command
Custom pulldown 101
Cell command
Assembly pulldown 96
Cell_display command
Assembly pulldown 96
Center command
Transform pulldown 91
Cerjan, C. J. 164
Change_directory command
Session pulldown 76
Charge command
Atom pulldown 113
Charges command
Forcefield pulldown 113
CHARMm command
Module pulldown 68
CharSize command
Graph pulldown 212
Grid pulldown 181
Charsize command
Contour pulldown 107
User pulldown 99
Clip command
Transform pulldown 92
Close command
Window pulldown 102
Close_Layout command
Window pulldown 103
Cluster command
Trajectory pulldown 201
methodology 205
color
use of 49
Color command
Contour pulldown 106
Graph pulldown 212
Grid pulldown 180
Molecule pulldown 83
User pulldown 98
color palette 28
Color table mode 50
COM_Distance_Def command
Trajectory pulldown 202
COM_P_Dist_n_Def command
Trajectory pulldown 203
command
Fragment pulldown 117
command modes
activate mode 32
repeat mode 32
commands
Completion_Status 219
concurrent 33
Control_Bkgd_Job 219
default objects 37
Define 129
Delete 129
escaping from typed to menu 32
Fuse_1 117
Fuse_3 119
Fuse_Close 120
hierarchy 17
Invert 124
Kill_Bkgd_Job 219
List 130
Merge 123
New 107
Open 107
Put 107
Rename 129
Setup_Bkgd_Job 219
typed 32
Unmerge 123
Completion_Status command, Background_Job pulldown 219
computational chemistry 1
Compute command
Grid pulldown 188
Confirmation command
Trajectory pulldown 213
Conformation command
Trajectory pulldown 200
conformational 139
search 5, 134, 157
Connect command
Transform pulldown 89
Construct_Graph command
Trajectory pulldown 195, 197, 201
methodology 204
Contour command
Graph pulldown 211
Grid pulldown 180
Contour pulldown 66
commands in 105
Contour utility
description 290
tutorial 294
coordinates
Cartesian vs. internal 163
coordination number 199
Copy command
Object pulldown 78
Subset pulldown 95
core
Viewer module 59
Correlate command
Graph pulldown 211
create
graph 207
Create command
Grid pulldown 188
cross-correlations 210
Császár, P. 167, 307
Custom pulldown 66
commands in 100
customization 21
cutoff
in calculating interaction energy 186
CVFF 183

D

DeCipher command
Module Pulldown 70
DeCipher module 17
default
changing object 38
object 18, 37
setting 101
Define command
Fragment pulldown 116
Subset pulldown 94, 95
Define command, Pseudo_Atom pulldown 129
Delete command
Atom pulldown 115
Fragment pulldown 116
Object pulldown 79
Subset pulldown 95
Delete command, Pseudo_Atom pulldown 129
DelPhi
grid output 105
DelPhi command
Module pulldown 67
DelPhi program
grid output 105
DepthCue command
Object pulldown 79
dials 12
Differentiation command
Graph pulldown 212
Dihedral command
Measure pulldown 87
Dihedral_Def command
Trajectory pulldown 202
Discover 5, 7
Discover command
Module pulldown 67
Discover program 193, 195, 197
and Forcefield pulldown commands 126
and out-of-plane atoms 114
and potential function atom types 127
initialize dynamics command 195
output for analysis 189
Discover program
input to Contour utility 291
rotors command 293
Discover_300 command
Module pulldown 67
Display command
Contour pulldown 106
Grid pulldown 179, 188
Molecule pulldown 83
Distance command
Measure pulldown 86
Distance_Def command
Trajectory pulldown 201
DMol command
Module pulldown 69
Docking 4
Docking command
Module pulldown 67
Docking module 17
tutorial 188
dynamical structural modification 198
dynamics trajectories
default time step 195

E

Edit command
Spectrum pulldown 100
Electron_Density command
AM_Analyze pulldown 179
Electronic_State command
AM_Setup pulldown 176
electrostatic 3
Element command
Modify pulldown 126
element test 339
Energy command
Measure pulldown 89
energy grid
calculating 183
energy minimization 116
Energy_Def command
Trajectory pulldown 203
ensemble average of any pair function 198
Env_var command
Session pulldown 75
Environment command
Session pulldown 71
environment variable
BIOSYM_LIBRARY 337
INSIGHT_POTENTIAL_TEMPLATES 337
environmental variable
BIOSYM_LIBRARY 114, 115, 128
FORCEFIELD 115, 128
INSIGHT_INIT_GLOBAL 23
INSIGHT_INIT_LOCAL 23, 24
INSIGHT_POTENTIAL_TEMPLATES 128
RESIDUE_LIBRARY 114, 128
WB_LOCAL_INIT 101
eps 300
equation
operators and operands 208
Equation command
Graph pulldown 208, 211
errors 54
Evaluate pulldown
commands in 187
for calculating interaction energy 186
examples
torsion input file 297, 298
Export 77
Export_Image command
File pulldown 78
Export_Molscript command
File pulldown 77
Export_Plot command
File pulldown 77
Export_Plot command
File pulldown 300

F

Family command
Trajectory pulldown 201
Fast Fourier Transform (FFT) 193
additional reading 197
algorithm 194, 196
limitations of 193
FFT_Real command
Graph pulldown 212
File Formats 309, 363
File pulldown 66
commands in 76
files
.arc 363, 372
.car 363
.cor 363
.eps 300
.grd 179
.inp 195
.mdf 364
.out 195
.pict 300
.tab 107
background_job_hosts 219
captopril_ s0.car 157
captopril_active.car 135
captopril_r.car 135
captopril_r.car2d 135
captopril_s.car 135, 144
captopril_s.car2d 135
captopril_s0.mdf 158
Cartesian coordinate file format 363
cvff.frc 346
frags.def 323
hbond_file.dat 331
history and archive from Discover 189
.hp 300
Insight II startup 220
intermediate plot file format 302
.ipf 300, 302, 303
molecular data file format 364
.ps 300
.qms 300
standard formatted file 297
torsion input file 298
Filter command
Trajectory pulldown 193, 200
methodology 204
Fletcher, R. 166, 307
focus parameter 29
Fogarasi, G. 163, 308
forcefield
AMBER 128, 358
CFF 128
CFF89 128
CHARMm 128
CVFF 128
definition 127
ESFF 128
library 114
specification 89
Forcefield pulldown
commands in 126
in Builder module 113
Forcefield/Potentials 143
forcefields 4
fragment library 115
Fragment pulldown
commands in 115
in Builder module 113
frequency filtering
explanation 193
function keys 14
F8 200
Fuse_1 command 117
Fuse_3 command 119
Fuse_Close command 120

G

generic pulldown
Background_Job 218
geometric
properties 129
Geometry command 123
geometry optimization
algorithms 164
constraints 163, 164
constraints, theory 166
dummy atoms 164
eigenvector following mode, derivation 164
eigenvector-following algorithm 163
fixed atoms 164
GDIIS 163
GDIIS method, theory 167
Hessian mode-following option 163
starting geometry 163
strategy 163
Get command
Contour pulldown 105
Fragment pulldown 115
Graph pulldown 210
Grid pulldown 179
Molecule pulldown 80
Spectrum pulldown 100
Subset pulldown 94, 95
Trajectory pulldown 193, 200
memory limitations 205
methodology 204
User pulldown 98
graph
cluster 189
inanimate 189, 190
multiple properties on 190
trajectory 189
usual method of creation 204
Graph pulldown
commands in 199, 207, 210
in Analysis module 199
tutorial 216
graph-generated contour file
input to Contour utility 292
grid file
input to Contour utility 291
Grid pulldown
command in 179, 187
Groups command
Forcefield pulldown 127

H

HBond command
Measure pulldown 88
Hehre, W. J. 163, 307
help 51
icon 73
XHelp 51
Help command
Session pulldown 73
Help pulldown 66, 103
Help Viewer 51
Hermann-Manguin
notation 364
Hewlett-Packard
output device 301
postscript 300
Histogram command
Grid pulldown 180
history 37
History command
Session pulldown 73
Homology command
Module pulldown 68
host
local 217
preference 220
remote 217
Hybridization command
Atom pulldown 113
hybridization test 340
hydrogens
forward and backward 324
naming scheme 114
Hydrogens command
Modify pulldown 121
equivalent to Hybridization Atom 114
hydrophobicity contrast function 198

I

icon palette 21
icons
customizing 21
pre-defined 19
Import 77
Inactive Stereoisomer 155
Info command
Graph pulldown 214
Inplot utility 300
Insight II startup file 220
Insight_Help 103
Integration command
Graph pulldown 212
interaction energy
equation incorporating nonbond and elec 184
Interface command
Subset pulldown 95
intermediate plot file format 302
intermolecular bonds
energies 187
Intermolecular command
Evaluate pulldown 187
Interpolation command
Graph pulldown 211
Invert command 124

J

job number 219

K

Kill_Bkgd_Job command, Background_Job pulldown 219

L

Label command
Contour pulldown 107
Graph pulldown 213
Grid pulldown 181
Molecule pulldown 83
User pulldown 99
Langridge reference 183
Layout command
Window pulldown 103
Layout_Template command
Window pulldown 102
Licensescommand
Module pulldown 70
Ligand_Design command
Module pulldown 68
Line_Fit command
Graph pulldown 211
LineWidth command
Object pulldown 80
link_pdb 319
List command
AM_Setup pulldown 176
Assembly pulldown 98
Atom pulldown 115
Contour pulldown 107
Folder pulldown 77
Grid pulldown 181
Molecule pulldown 85
Object pulldown 80
Spectrum pulldown 100
Subset pulldown 96
User pulldown 100
List command, Pseudo_Atom pulldown 130
List_Properties command
Custom pulldown 101
log file
WBLOGFILE 76
logfile
insight.log 23
WBLOGFILE 23
WBLOGFILE.save 23
Lower command
Window pulldown 102
Lower_Layout command
Window pulldown 103

M

Macro_Delete command
Custom pulldown 101
Macromolecule structures 2
macros
with Custom pulldown 100
MBOND command
Module pulldown 68
Measure pulldown 66
commands in 86
Measure/Distance 151, 152, 156
Measure/Energy 151, 152, 155, 157
memory
limitations 205
Merge command 123
metal binding sites in proteins 198
methyl
group 147, 155
Miller, W. H. 164
Modify pulldown
commands in 117
in Builder module 113
Modify/Invert 155
Modify_Display command
Graph pulldown 213
Module 136, 145
Module pulldown 66
commands in 66
MolBuilder 2
molecular dynamics 4
simulation 198
Molecular Graphics 1
molecular mechanics 3, 4, 6
output to analysis 199
Molecular modeling 1
Molecular_Orbital command
AM_Analyze pulldown 179
Molecule pulldown 66
commands in 80
Molecule/Get 157
Molecule/Put 144, 150, 155, 157
Monitor_Style command
Measure pulldown 87
mouse functions 11
Move command
Transform pulldown 91
Move_Axis command
Graph pulldown 213

N

naming scheme
file/function 209
fragments 323
hydrogens 114
plots 209
space group 333
Neighbor command
Measure pulldown 88
New command, Table pulldown 107
New_Molecule 107
NMR
experiments 5
NMR_Refine command
Module pulldown 68
nonbond potential energy
6-12 equation 183
6-9 equation 185
nongraphics mode 22
non-standard
input to Contour utility 294
Nyquist sampling rate 195

O

object names 41
atom level 43
monomer/residue level 42
object level 41
parentheses in 45
wildcards in 46
Object pulldown 66
commands in 78
Object/Delete 150
Object/Rename 156
objects 38
assemblies 40
contours 39
graphs 40
molecules 38
spectrums 40
user objects 39
Open command, Table pulldown 107
operands
for equations 209
operators
for equations 208
Optimize 4, 143, 150, 151, 156, 157
Optimize command
AM_Parameters pulldown 177
Optimize pulldown 130
Optimize pulldown
commands in 130
in Builder module 113
Overlay command
Transform pulldown 93

P

parameter block
building with Custom pulldown 101
description 25
non-typable 26
parameters
default values 30
enumerated choice 26, 36
focus 29
inactive 30
list 26, 36
on/off (Boolean) 26, 34
trigger 31
typable 26
Pattabiraman et al. reference 183
Pattabiramin et al. reference 191
pharmacophore 134, 156
pattern 133, 157
pict
output device 300
Pilot 57
Pilot_Tutorials 105
Planar command
Atom pulldown 114
plots
naming scheme 209
polymers 116
Position command
Transform pulldown 90
postscript
device 300
output device 301
Potential command
Atom pulldown 114
potential function atom type 114, 127
potential template rule file 127
Potential Template Rules
appendix 127
potential template rules 337
potential type template file
cvff_templates.dat 346
Potentials command
Forcefield pulldown 114, 127
PP_Ang_3_Def command
Trajectory pulldown 202
PP_Ang_n_Def command
Trajectory pulldown 202
pP_Dist_3_Def command
Trajectory pulldown 202
pP_Dist_n_Def command
Trajectory pulldown 203
precedence tree 340
pre-defined icons 19
Press et al. reference 192
printers
postscript 300
qms 300
pseudo atoms
defined 44
Pseudo_Atom pulldown
commands in 129, 203
in Analysis module 199
Pulay, P. 163, 167, 307, 308
pulldowns
Background_Job 218
Put command
Contour pulldown 105, 106
Fragment pulldown 116
Graph pulldown 210, 211
Grid pulldown 179
Molecule pulldown 82
Spectrum pulldown 100
Trajectory pulldown 200
Put command, Table pulldown 107

Q

qms
output device 300
QuanteMM 69
quantum mechanics 5
calculations 6
Quit command
Session pulldown 76

R

R stereoisomer 155
radial distribution function 198
Raise command
Window pulldown 102
Raise_Layout command
Window pulldown 103
RDF 198
Remove command
Assembly pulldown 96
Folder pulldown 77
Fragment pulldown 116
Rename command
Atom pulldown 115
Object pulldown 79
Rename command, Pseudo_Atom pulldown 129
Render command
Molecule pulldown 84
Repartition_Cluster command
Trajectory pulldown 201
Repeat command
Fragment pulldown 116
Repeat command
Residue pulldown 324
Replace command
Atom pulldown 115
Reset command
Transform pulldown 90
residue
library 114
residue library 127
Restore_Folder command
File pulldown 77
RGB mode 50
Ribbon command
Molecule pulldown 84
RMS value
as basis for clustering 197
Rock command
Transform pulldown 92
Rotate command
Transform pulldown 91
Run command
AM_Run pulldown 178

S

Saddle command
AM_Parameters pulldown 177
Save command
Folder pulldown 76
Scale command
Transform pulldown 91
Scale_Axis command
Graph pulldown 213
SCF command
AM_Parameters pulldown 177, 178
Schrodinger equation 6
Search_Compare 157
Search_Compare command
Module pulldown 68
SecondaryRender command
Molecule pulldown 84
Select command
Forcefield pulldown 126
Session pulldown 66
commands in 70
Set_Defaults command
Molecule pulldown 82
Setup_Bkgd_Job command, Background_Job pulldown 219
Shepard, R. 307
side chain conformation 154
Simons, J. 307
Sketch 2, 113, 151
sketch facility 39
Sketch pulldown 133
Sketch/Edit 146
Sketch/Get 149, 155
Sketch/Put 148, 157
Sketcher 133
slab
also called viewing window 92
position 12, 14, 92
thickness 12, 92
Sleep command
Session pulldown 76
Slice command
Grid pulldown 180
Smoothing command
Graph pulldown 212
Soak command
Assembly pulldown 97
Solvation command
Module pulldown 67
Source_File command
File pulldown 23, 78
Spectra pulldown
in Analysis module 199
Spectrum pulldown 66
commands in 100
spectrums 40
standard unformatted
input to Contour utility 293
Stereo command
Session pulldown 75
stereochemistry 148
Store command
Transform pulldown 90
subpixel 71
Subset pulldown 66
commands in 94
Superimpose command
Transform pulldown 94, 197
Surface Molecule 84
Symmetry command
Assembly pulldown 97
System command
AM_Setup pulldown 175

T

tables
atom record definition 366
B-8, pseudo atom set definition 371
F-1, out-of-plane assignment rules 358
pseudo atom definition 370
torsion record definition 369
Tabulate command
Molecule pulldown 85
Trajectory pulldown 203
Taylor, P. W. 308
template
out-of-plane assignment 357
potential template rule file 127
potential type 337
textport 8
Threshold command
Graph pulldown 214
Tick_Mark command
Graph pulldown 214
Torsion command
Transform pulldown 92
torsion file
input to Contour utility 293
Trajectory pulldown 207
commands in 199
in Analysis module 199
Transform pulldown 66
commands in 89
Transform/Torsion 151, 153, 155
Transparency command
Molecule pulldown 83
User pulldown 98
Trigger command
Custom pulldown 101
Turbomole command
Module pulldown 69
tutorial
Ampac/Mopac 181
Analysis module 205
Builder module 130
Docking module 188
Graph pulldown 216
Viewer module 111

U

Unanimate command
Trajectory pulldown 200
UNIX 135
commands 23
Unix command
Session Pulldown 300
Session pulldown 76
Unmerge command 123
User pulldown 66
commands in 98

V

value-aid 27
color palette 28
description 27
van der Waals
attraction 3
electrostatic (Coulombic) 152
repulsion 3
Viewer 2
Viewer module 17
pulldowns in 66
tutorial 111

W

weight factors for each atom 198
Window pulldown 66, 102

X

x-ray crystal refinement
grid output 105
XSight 68
XYZ command
Measure pulldown 87

Z

Zhou, X. 308
zinc metallopeptidase 133
Zindo command
Module pulldown 69
Z-matrix 163
Zone command
Subset pulldown 94


Index



Last updated December 17, 1998 at 04:29PM PST.
Copyright © 1998, Molecular Simulations Inc. All rights reserved.