Insight II

Index

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A

ACE

Inhibitor Captopril 1

pharmacophore model 19

Activity_Prediction command

Module pulldown 8

Adams, N. 1

Add command

Assembly pulldown 38

Add_To_Pulldown command

Custom pulldown 43

Aldehyde 6

fragment 6

Alias command

Session pulldown 16

AM_Analyze pulldown

commands in 20

AM_Parameters pulldown

commands in 18

AM_Run pulldown

commands in 20

AM_Setup pulldown

commands in 17

amide

bond 6, 15, 20, 24

Ampac/Mopac 6

Ampac/Mopac command

Module pulldown 10

Ampac/Mopac module 11

tutorial 23

Analysis 5

Analysis command

Module pulldown 11

Analysis module 11

tutorial 17

Angiotensin Converting Enzyme (ACE) 1

Angle command

Measure pulldown 29

Angle_Def command

Trajectory pulldown 14

Animate command

Trajectory pulldown 7, 12

memory limitations 17

methodology 17

Annotate command

User pulldown 40

Apply command

Transform pulldown 33

aromaticity test 4

assembly

equivalent to family 13

Assembly pulldown 7

commands in 37

Assimilate 6

Associate command

Assembly pulldown 38

Atom pulldown

commands in 1

in Builder module 1

atom tests 3

auto-correlations 4

average plane evaluation 3

Axes command

Transform pulldown 32

Axes_Display command

Object pulldown 21

Axis_Function command

Trajectory pulldown 13

methodology 16

background color 13

background job

completion status 4

default mode 3

execution mode 4

host 4

requirements for running on a remote host 1

Background_Job

application 2

command summary 2

commands in 19, 15, 2

methodology 3

Background_Job pulldown

commands in 19, 15

in Analysis module 11

Background_Job tutorial

using the Ampac/Mopac module 5

Baker, J. 5, 6, 1

Banerjee, A. 6, 1

Bergeron, D. 6, 1

Biopolymer command

Module pulldown 8

Biopolymer module 11

Biosym Command Language

see also BCL 1

with Custom pulldown 42

Blank command

Object pulldown 21

Blink command

Object pulldown 21

Bond_Order command

Molecule pulldown 25

Boolean command

Graph pulldown 5

Bracewell

reference 6

Brookhaven

Protein Data Bank 2

Brookhaven database

molecule from 32

Browse command

Molecule pulldown 27

Buffer command

Session pulldown 16

Builder 2, 4, 2, 4, 13, 19

Builder command

Module pulldown 8

Builder module 11

Builder module 1

Builder tutorial 18

bulk density 10, 11

Bump command

Measure pulldown 29

Button command

Session pulldown 17

Calculation command

AM_Setup pulldown 18

Cambridge

data files 2

Cambridge Crystal database

molecule from 32

Captopril 2, 3, 17

Using Sketch 13

carboxyl

group 2, 15, 16, 20, 21, 24

oxygen 20

case sensitivity 18

Catalogue command

Custom pulldown 43

Cell command

Assembly pulldown 38

Cell_display command

Assembly pulldown 38

Center command

Transform pulldown 32

Cerjan, C. J. 6

Change_directory command

Session pulldown 18

Charge command

Atom pulldown 1

Charges command

Forcefield pulldown 1

CHARMm command

Module pulldown 10

CharSize command

Graph pulldown 6

Grid pulldown 22

Charsize command

Contour pulldown 48

User pulldown 41

Clip command

Transform pulldown 33

Close command

Window pulldown 44

Close_Layout command

Window pulldown 45

Cluster command

Trajectory pulldown 13

methodology 17

color

use of 43

Color command

Contour pulldown 48

Graph pulldown 6

Grid pulldown 21

Molecule pulldown 25

User pulldown 40

color palette 22

Color table mode 44

COM_Distance_Def command

Trajectory pulldown 14

COM_P_Dist_n_Def command

Trajectory pulldown 15

command

Fragment pulldown 5

command modes

activate mode 26

repeat mode 26

commands

Completion_Status 3

concurrent 27

Control_Bkgd_Job 3

default objects 31

Define 17

Delete 17

escaping from typed to menu 26

Fuse_1 5

Fuse_3 7

Fuse_Close 8

hierarchy 11

Invert 12

Kill_Bkgd_Job 3

List 18

Merge 11

New 49

Open 49

Put 49

Rename 17

Setup_Bkgd_Job 3

typed 26

Unmerge 11

Completion_Status command, Background_Job pulldown 3

computational chemistry 1

Compute command

Grid pulldown 6

Confirmation command

Trajectory pulldown 7

Conformation command

Trajectory pulldown 12

conformational 7

search 5, 2, 25

Connect command

Transform pulldown 31

Construct_Graph command

Trajectory pulldown 7, 9, 13

methodology 16

Contour command

Graph pulldown 5

Grid pulldown 22

Contour pulldown 8

commands in 46

Contour utility

description 2

tutorial 6

coordinates

Cartesian vs. internal 5

coordination number 11

Copy command

Object pulldown 20

Subset pulldown 37

core

Viewer module 1

Correlate command

Graph pulldown 5

create

graph 1

Create command

Grid pulldown 6

cross-correlations 4

Császár, P. 9, 1

Custom pulldown 7

commands in 42

customization 15

cutoff

in calculating interaction energy 4

CVFF 1

DeCipher command

Module Pulldown 11

DeCipher module 11

default

changing object 32

object 12, 31

setting 43

Define command

Fragment pulldown 4

Subset pulldown 36, 37

Define command, Pseudo_Atom pulldown 17

Delete command

Atom pulldown 3

Fragment pulldown 4

Object pulldown 21

Subset pulldown 37

Delete command, Pseudo_Atom pulldown 17

DelPhi

grid output 46

DelPhi command

Module pulldown 9

DelPhi program

grid output 46

DepthCue command

Object pulldown 21

dials 6

Differentiation command

Graph pulldown 6

Dihedral command

Measure pulldown 29

Dihedral_Def command

Trajectory pulldown 14

Discover 5, 1

Discover command

Module pulldown 9

Discover program 5, 7, 9

and Forcefield pulldown commands 14

and out-of-plane atoms 2

and potential function atom types 15

initialize dynamics command 7

output for analysis 1

Discover program

input to Contour utility 3

rotors command 5

Discover_300 command

Module pulldown 9

Display command

Contour pulldown 48

Grid pulldown 21, 6

Molecule pulldown 25

Distance command

Measure pulldown 28

Distance_Def command

Trajectory pulldown 13

DMol command

Module pulldown 11

Docking 4

Docking command

Module pulldown 9

Docking module 11

tutorial 6

dynamical structural modification 10

dynamics trajectories

default time step 7

Edit command

Spectrum pulldown 42

Electron_Density command

AM_Analyze pulldown 20

Electronic_State command

AM_Setup pulldown 17

electrostatic 3

Element command

Modify pulldown 14

element test 3

Energy command

Measure pulldown 30

energy grid

calculating 1

energy minimization 4

Energy_Def command

Trajectory pulldown 15

ensemble average of any pair function 10

Env_var command

Session pulldown 17

Environment command

Session pulldown 12

environment variable

BIOSYM_LIBRARY 1

INSIGHT_POTENTIAL_TEMPLATES 1

environmental variable

BIOSYM_LIBRARY 2, 3, 16

FORCEFIELD 3, 16

INSIGHT_INIT_GLOBAL 17

INSIGHT_INIT_LOCAL 17, 18

INSIGHT_POTENTIAL_TEMPLATES 16

RESIDUE_LIBRARY 2, 16

WB_LOCAL_INIT 42

eps 12

equation

operators and operands 2

Equation command

Graph pulldown 2, 5

errors 48

Evaluate pulldown

commands in 5

for calculating interaction energy 4

examples

torsion input file 9, 10

Export 19

Export_Image command

File pulldown 20

Export_Plot command

File pulldown 19

Export_Plot command

File pulldown 12

Family command

Trajectory pulldown 13

Fast Fourier Transform (FFT) 5

additional reading 9

algorithm 6, 8

limitations of 5

FFT_Real command

Graph pulldown 6

File Formats 1

File pulldown 7

commands in 18

files

.arc 1, 10

.car 1

.cor 1

.eps 12

.grd 20

.inp 7

.mdf 2

.out 7

.pict 12

.tab 49

background_job_hosts 3

captopril_ s0.car 25

captopril_active.car 3

captopril_r.car 3

captopril_r.car2d 3

captopril_s.car 3, 12

captopril_s.car2d 3

captopril_s0.mdf 26

Cartesian coordinate file format 1

cvff.frc 10

frags.def 1

hbond_file.dat 1

history and archive from Discover 1

.hp 12

Insight II startup 4

intermediate plot file format 14

.ipf 12, 14, 15

molecular data file format 2

.ps 12

.qms 12

standard formatted file 9

torsion input file 10

Filter command

Trajectory pulldown 5, 12

methodology 16

Fletcher, R. 8, 1

focus parameter 23

Fogarasi, G. 5, 2

forcefield

AMBER 16, 22

CFF 16

CFF89 16

CHARMm 16

CVFF 16

definition 15

ESFF 16

library 2

specification 30

Forcefield pulldown

commands in 14

in Builder module 1

Forcefield/Potentials 11

forcefields 4

fragment library 3

Fragment pulldown

commands in 3

in Builder module 1

frequency filtering

explanation 5

function keys 8

F8 12

Fuse_1 command 5

Fuse_3 command 7

Fuse_Close command 8

generic pulldown

Background_Job 2

geometric

properties 17

Geometry command 11

geometry optimization

algorithms 5

constraints 5

constraints, theory 8

dummy atoms 6

eigenvector following mode, derivation 6

eigenvector-following algorithm 5

fixed atoms 6

GDIIS 5

GDIIS method, theory 9

Hessian mode-following option 5

starting geometry 5

strategy 5

Get command

Contour pulldown 47

Fragment pulldown 3

Graph pulldown 4

Grid pulldown 21

Molecule pulldown 22

Spectrum pulldown 42

Subset pulldown 36, 37

Trajectory pulldown 5, 12

memory limitations 17

methodology 16

User pulldown 40

graph

cluster 1

inanimate 1, 2

multiple properties on 2

trajectory 1

usual method of creation 16

Graph pulldown

commands in 11, 1, 4

in Analysis module 11

tutorial 10

graph-generated contour file

input to Contour utility 4

grid file

input to Contour utility 3

Grid pulldown

command in 20, 5

Groups command

Forcefield pulldown 15

HBond command

Measure pulldown 30

Hehre, W. J. 5, 1

help 45

icon 15

XHelp 45

Help command

Session pulldown 15

Help pulldown 7, 45

Help Viewer 45

Hermann-Manguin

notation 2

Hewlett-Packard

output device 13

postscript 12

Histogram command

Grid pulldown 21

history 31

History command

Session pulldown 15

Homology command

Module pulldown 10

host

local 1

preference 4

remote 1

Hybridization command

Atom pulldown 1

hybridization test 4

hydrogens

forward and backward 2

naming scheme 2

Hydrogens command

Modify pulldown 9

equivalent to Hybridization Atom 2

hydrophobicity contrast function 10

icon palette 15

icons

customizing 15

pre-defined 13

Import 19

Inactive Stereoisomer 23

Info command

Graph pulldown 8

Inplot utility 12

Insight II startup file 4

Insight_Help 45

Integration command

Graph pulldown 6

interaction energy

equation incorporating nonbond and elec 2

Interface command

Subset pulldown 36

intermediate plot file format 14

intermolecular bonds

energies 5

Intermolecular command

Evaluate pulldown 5

Interpolation command

Graph pulldown 5

Invert command 12

job number 3

Kill_Bkgd_Job command, Background_Job pulldown 3

Label command

Contour pulldown 48

Graph pulldown 7

Grid pulldown 22

Molecule pulldown 25

User pulldown 41

Langridge reference 1

Layout command

Window pulldown 44

Layout_Template command

Window pulldown 44

Licensescommand

Module pulldown 12

Ligand_Design command

Module pulldown 9

Line_Fit command

Graph pulldown 5

LineWidth command

Object pulldown 22

link_pdb 9

List command

AM_Setup pulldown 18

Assembly pulldown 40

Atom pulldown 3

Contour pulldown 49

Folder pulldown 19

Grid pulldown 22

Molecule pulldown 27

Object pulldown 22

Spectrum pulldown 42

Subset pulldown 37

User pulldown 41

List command, Pseudo_Atom pulldown 18

List_Properties command

Custom pulldown 43

log file

WBLOGFILE 18

logfile

insight.log 17

WBLOGFILE 16

WBLOGFILE.save 17

Lower command

Window pulldown 44

Lower_Layout command

Window pulldown 45

Macro_Delete command

Custom pulldown 43

Macromolecule structures 2

macros

with Custom pulldown 42

MBOND command

Module pulldown 10

Measure pulldown 7

commands in 28

Measure/Distance 19, 20, 24

Measure/Energy 19, 20, 23, 25

memory

limitations 17

Merge command 11

metal binding sites in proteins 10

methyl

group 15, 23

Miller, W. H. 6

Modify pulldown

commands in 5

in Builder module 1

Modify/Invert 23

Modify_Display command

Graph pulldown 7

Module 4, 13

Module pulldown 7

commands in 8

MolBuilder 2

molecular dynamics 4

simulation 10

Molecular Graphics 1

molecular mechanics 3, 4, 6

output to analysis 11

Molecular modeling 1

Molecular_Orbital command

AM_Analyze pulldown 20

Molecule pulldown 7

commands in 22

Molecule/Get 25

Molecule/Put 12, 18, 23, 25

Monitor_Style command

Measure pulldown 29

mouse functions 5

Move command

Transform pulldown 33

Move_Axis command

Graph pulldown 7

naming scheme

file/function 3

fragments 1

hydrogens 2

plots 3

space group 1

Neighbor command

Measure pulldown 30

New command, Table pulldown 49

New_Molecule 49

NMR

experiments 5

NMR_Refine command

Module pulldown 10

nonbond potential energy

6-12 equation 1

6-9 equation 3

nongraphics mode 16

non-standard

input to Contour utility 6

Nyquist sampling rate 7

object names 35

atom level 37

monomer/residue level 36

object level 35

parentheses in 39

wildcards in 39

Object pulldown 7

commands in 20

Object/Delete 18

Object/Rename 24

objects 32

assemblies 33

contours 33

graphs 34

molecules 32

spectrums 34

user objects 33

Open command, Table pulldown 49

operands

for equations 3

operators

for equations 2

Optimize 4, 11, 18, 19, 24, 25

Optimize command

AM_Parameters pulldown 18

Optimize pulldown 18

Optimize pulldown

commands in 18

in Builder module 1

Overlay command

Transform pulldown 35

parameter block

building with Custom pulldown 43

description 19

non-typable 20

parameters

default values 24

enumerated choice 20, 30

focus 23

inactive 24

list 20, 30

on/off (Boolean) 20, 28

trigger 25

typable 19

Pattabiraman et al. reference 1

Pattabiramin et al. reference 3

pharmacophore 2, 24

pattern 1, 25

pict

output device 12

Pilot 1

Pilot_Tutorials 46

Planar command

Atom pulldown 2

plots

naming scheme 3

polymers 4

Position command

Transform pulldown 32

postscript

device 12

output device 13

Potential command

Atom pulldown 2

potential function atom type 2, 15

potential template rule file 15

Potential Template Rules

appendix 15

potential template rules 1

potential type template file

cvff_templates.dat 10

Potentials command

Forcefield pulldown 2, 15

PP_Ang_3_Def command

Trajectory pulldown 14

PP_Ang_n_Def command

Trajectory pulldown 14

pP_Dist_3_Def command

Trajectory pulldown 14

pP_Dist_n_Def command

Trajectory pulldown 15

precedence tree 4

pre-defined icons 13

Press et al. reference 4

printers

postscript 12

qms 12

pseudo atoms

defined 38

Pseudo_Atom pulldown

commands in 17, 15

in Analysis module 11

Pulay, P. 5, 9, 1, 2

pulldowns

Background_Job 2

Put command

Contour pulldown 47

Fragment pulldown 4

Graph pulldown 4, 5

Grid pulldown 21

Molecule pulldown 24

Spectrum pulldown 42

Trajectory pulldown 12

Put command, Table pulldown 49

qms

output device 12

QuanteMM 11

quantum mechanics 5

calculations 6

Quit command

Session pulldown 18

R stereoisomer 23

radial distribution function 10

Raise command

Window pulldown 44

Raise_Layout command

Window pulldown 45

RDF 10

Remove command

Assembly pulldown 38

Folder pulldown 19

Fragment pulldown 4

Rename command

Atom pulldown 3

Object pulldown 21

Rename command, Pseudo_Atom pulldown 17

Render command

Molecule pulldown 26

Repartition_Cluster command

Trajectory pulldown 13

Repeat command

Fragment pulldown 4

Repeat command

Residue pulldown 2

Replace command

Atom pulldown 3

Reset command

Transform pulldown 32

residue

library 2

residue library 15

Restore_Folder command

File pulldown 19

RGB mode 44

Ribbon command

Molecule pulldown 26

RMS value

as basis for clustering 9

Rock command

Transform pulldown 34

Rotate command

Transform pulldown 33

Run command

AM_Run pulldown 20

Saddle command

AM_Parameters pulldown 19

Save command

Folder pulldown 18

Scale command

Transform pulldown 33

Scale_Axis command

Graph pulldown 7

SCF command

AM_Parameters pulldown 18, 19

Schrodinger equation 6

Search_Compare 25

Search_Compare command

Module pulldown 10

SecondaryRender command

Molecule pulldown 26

Select command

Forcefield pulldown 14

Session pulldown 7

commands in 12

Set_Defaults command

Molecule pulldown 24

Setup_Bkgd_Job command, Background_Job pulldown 3

Shepard, R. 1

side chain conformation 22

Simons, J. 1

Sketch 2, 1, 19

sketch facility 32

Sketch pulldown 1

Sketch/Edit 14

Sketch/Get 17, 23

Sketch/Put 16, 25

Sketcher 1

slab

also called viewing window 33

position 6, 8, 33

thickness 6, 33

Sleep command

Session pulldown 18

Slice command

Grid pulldown 22

Smoothing command

Graph pulldown 6

Soak command

Assembly pulldown 39

Solvation command

Module pulldown 9

Source_File command

File pulldown 17, 20

Spectra pulldown

in Analysis module 11

Spectrum pulldown 7

commands in 41

spectrums 34

standard unformatted

input to Contour utility 5

Stereo command

Session pulldown 17

stereochemistry 16

Store command

Transform pulldown 32

subpixel 13

Subset pulldown 7

commands in 36

Superimpose command

Transform pulldown 35, 9

Surface Molecule 26

Symmetry command

Assembly pulldown 39

System command

AM_Setup pulldown 17

tables

atom record definition 4

B-8, pseudo atom set definition 9

F-1, out-of-plane assignment rules 22

pseudo atom definition 8

torsion record definition 7

Tabulate command

Molecule pulldown 27

Trajectory pulldown 15

Taylor, P. W. 2

template

out-of-plane assignment 21

potential template rule file 15

potential type 1

textport 2

Threshold command

Graph pulldown 8

Tick_Mark command

Graph pulldown 8

Torsion command

Transform pulldown 34

torsion file

input to Contour utility 5

Trajectory pulldown 1

commands in 11

in Analysis module 11

Transform pulldown 7

commands in 31

Transform/Torsion 19, 21, 23

Transparency command

Molecule pulldown 25

User pulldown 40

Trigger command

Custom pulldown 43

Turbomole command

Module pulldown 11

tutorial

Ampac/Mopac 23

Analysis module 17

Builder module 18

Docking module 6

Graph pulldown 10

Viewer module 53

Unanimate command

Trajectory pulldown 12

UNIX 3

commands 17

Unix command

Session Pulldown 12

Session pulldown 18

Unmerge command 11

User pulldown 7

commands in 40

value-aid 21

color palette 22

description 21

van der Waals

attraction 3

electrostatic (Coulombic) 20

repulsion 3

Viewer 2

Viewer module 11

pulldowns in 7

tutorial 53

weight factors for each atom 10

Window pulldown 7, 43

x-ray crystal refinement

grid output 46

XSight 10

XYZ command

Measure pulldown 29

Zhou, X. 2

zinc metallopeptidase 1

Zindo command

Module pulldown 11

Z-matrix 5

Zone command

Subset pulldown 36