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Index

Analysis module, 5-14

background jobs

completion status, 5-18

default mode, 5-17

electronic mail notification, 5-18

execution mode, 5-18

job number, 5-17

local host, 3-5

monitoring, 5-19, 5-20

notification window, 5-18

parameters, 4-4

preferred host, 5-18

remote host, requirements, 3-6

saving command file, 5-18

stopping execution, 5-20

Background_Job pulldown, 4-9, 5-13

Background_Job, pulldown, 1-1

Background_Job/Completion_Status command, 5-14

Background_Job/Setup_Bkgd_Job command, 5-13

BFGS, 2-9

commands

documentation format, 1-3

entering on command line in Insight, 1-3

conformational search

initiating, 4-6

conformations

displaying, 4-8

estimating number of, 4-6, 5-19

Conformer pulldown, 1-2, 4-8, 5-34

conformers

boolean operations on, 5-35

eliminating duplicates, 3-4

modifying current list, 5-36

selecting, 5-35

selecting associated vectors, 5-35

specifying frames for boolean, 5-35

specifying parameters for boolean from file, 5-35

Conformer/Display command, 4-8, 5-34

DeCipher module, 5-14

Discover, use in calculating and minimizing conformer energy, 2-9

distance constraints, 1-2

creating a list of, 4-4

distance definition, 5-31

distance maps, 1-2, 2-7

applying boolean operations, 4-8, 5-29, 5-30

constructing from trajectory, 5-31

creating from prior search, 5-28

creating without initiating a search, 5-27

definition, 2-7

graphing, 4-8, 5-31

illustration, 2-8

prior search, constraining with, 5-23

setting up, 4-5

specifications, editing, 5-24

specifications, viewing, 5-24

specifying, 5-23

using in series, 2-7

Distance_Map pulldown, 1-2, 4-8

Distance_Map/Boolean command, 4-8

Distance_Map/Construct_Graph command, 4-8

duplicate removal

customizing, 4-5

electrostatic potential

fitting, optional features, 5-12

similarities, 1-1

similarities calculation, 2-3

energy

calculation, 5-25

calculation and screening, 4-5

calculation options, 5-26

controlling minimization process, 5-25

minimization, 5-25

field similarity

calculation types, 5-12

files

.arc, 5-21

background_job_hosts, 5-17

binary, 3-6

.scs_prm, 5-15, 5-16

.scs_tor, 5-16

text, 3-6

.xdr_tor, 5-16, 5-21

Gaussian function

in the electrostatic calculation, 3-2

Graph pulldown, 1-2, 4-9

graphical response time, 5-7

help, on-line, 1-3

Hodgkin index, 2-3

implicit torsion

use in conformational ring search, 3-3

molecular field simlarity, 2-1

molecular fields

comparing, 4-3

Overlap pulldown, 1-1, 2-1, 5-8

algorithm, 3-1

Overlap/Define command, 4-3

Overlap/Display command, 4-3

Overlap/Field_Fit command, 4-3

resolution, of distance definitions, 5-29

ring closure bonds

specifying cleavage of, 3-3

ring closure bonds, creating and editing, 4-4

rms fitting, 1-1, 2-1

rotatable bonds, interactive mode, 5-15

SC_Search pulldown, 1-1, 4-4, 5-13

SC_Search/Load command, 4-6, 5-3, 5-14

SC_Search/Scale_Radii command, 4-5, 5-13, 5-16

SC_Search/SCS_Run command, 4-6, 5-14

SC_Search/Set_Distance command, 4-4, 5-13, 5-16

SC_Search/Set_Dist_Map command, 4-5, 5-13

SC_Search/Set_Energy_Params command, 4-5, 5-13

SC_Search/Set_Filter_Params command, 4-5

SC_Search/Set_Ring_Closure command, 4-4

SC_Search/Set_Rot_Bond command, 4-4, 5-13, 5-14

search, processing previous, 4-6

Search_Compare

overview, 1-1

starting, 1-2

summary, 1-1

similarity calculation and optimization

equation for multiple molecules, 2-3

Spreadsheet pulldown, 1-2

superimposing molecules, 2-1, 4-3, 5-1

assembly, forming an, 5-11

atomic correspondences, 5-8

color, use of, 5-11

equation minimized, 2-1

executing the calculation, 5-11

highlighting, 5-8

more than two molecules, 5-9

rms difference in atomic coordinates, 5-12

rotatable bonds, 5-10

setting up, 5-8

specifications, chains of, 5-11

specifications, checking, 5-10

specifications, editing, 5-10

specifications, linked, 5-11

systematic conformational searches, 5-13

advanced searches, 5-21

analyzing results, 2-9, 4-6, 5-14

anchor atom, 5-19, 5-27

combining criteria, 5-27

distance constraints, 5-14

distance constraints, creating list, 5-16

distance constraints, editing list, 5-16

distance constraints, reviewing list, 5-17

distance maps, 5-23

duplicate conformers, 5-25

energy and, 5-24

energy criteria, 2-9, 3-4

estimating number of conformations, 5-19, 5-26

files, 5-27

initiating a standard search, 5-19

initiating an advanced search, 5-26

limiting number of generated conformers, 2-6, 2-7, 2-9, 5-24

loading results, 4-6

method, 2-6

parameters, 4-4, 5-14

post-processing, 5-28

prior input file, using, 4-4, 5-14, 5-16

procedure, 5-13

radius scaling, 5-14

results, files, 5-21

results, loading into the Insight II program, 5-21

rotatable bonds, 5-14

rotatable bonds, creating list, 4-4, 5-14

rotatable bonds, editing list, 5-14, 5-15

rotatable bonds, reviewing list, 5-15

setting up, 4-4, 5-14, 5-23, 5-24

stable conformers, 5-24

standard searches, 5-14

steric clashes, 5-16

trajectory, 5-21

systematic conformational searching

on ring systems, 3-2

trajectories

aligning with molecule or assembly, 5-3

loading into the Insight II program, 5-3, 5-32

Trajectory/Get command, 5-3

van der Waals radii, 3-1, 4-5, 5-3, 5-16

vector maps, 5-32

Boolean operations on, 5-35

color, 5-33

correspondence with trajectory frames, 3-5

creating, 5-32

defining, 5-32

definition of, 2-10

display, 5-33

display of individual vectors, 5-33

displaying associated conformers, 5-34

energy, 5-34

information, 5-32

labels, 5-33

manipulating lists of conformations, 5-34

requirements, 5-32

saving lists of conformers, 5-34

selecting conformers in, 5-35

Vector_Map pulldown, 1-2, 4-7, 5-32

Vector_Map/Color command, 4-7

Vector_Map/Create command, 4-7

Vector_Map/Display_Vector command, 4-7

Vector_Map/Label command, 4-7

Vector_Map/List command, 4-7

Volume pulldown, 1-1, 4-1, 5-1

volumes

algorithm, 3-1, 5-2

aligning, 4-2

aligning with molecules, 5-1

assemblies, 5-2, 5-3, 5-4

Boolean operations, 4-1, 5-5

border, 5-2

calculating, 4-1, 5-4

cancelling a calculation, 5-7

color, 5-7

contour, 5-4

creating, 4-1, 5-2

cubic angstroms, 4-2, 5-5, 5-6

deleting, 5-6

difference, 5-5

displaying components, 4-2

displaying old volumes, 5-6

exclusive-or, 5-5

grid, 3-1, 5-2, 5-6

grid resolution, 5-5

grids, 4-2

intersection, 5-5

labeling, 5-7

molecules, 5-2, 5-4

point cloud, 5-7

relative size, 5-3

setting up for, 5-1

solid contour, 5-4, 5-7

specifications for, 5-1

trajectories, 5-2, 5-3, 5-4

union, 5-4, 5-5

wildcards, 5-2, 5-5

wire-frame contour, 5-4, 5-7

Volume/Align command, 4-2

Volume/Boolean command, 4-1

Volume/Color command, 4-2

Volume/Create command, 4-1

Volume/Display command, 4-2

Volume/Grid_Setup command, 4-2

Volume/Label command, 4-2

Volume/List command, 4-2