C: Sub Index for SYBYL and UNITY Documentation


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


C-alpha carbon global set
C chromosome
C-terminal groups
partial charges
Calculate
similarity score
VDW energy
volume overlap
Calculate fingerprints in parallel
Callback creation
Cap atoms
adding to terminal residues
Cap global set
CAPTURE
Carbohydrate
building
Cartesian coordinates
Cartridge contents
Cavity
building the ligand
FlexX
Surflex-Dock
creating file
depth parameters
placing the base fragment in the model
locating
CCR
optimization limit
relaxation limit
threshold
threshold for errors
CDF file
creating
Cell
modifying
selecting via the menubar
Cell-based visualization tools
DiverseSolutions addons
Cell contents MSS
DiverseSolutions addons
Center
Center of mass
Center of mass
data record in mol2 file
VISUALIZE
Centerview
Centroid
feature
TAILOR
Centroid
data record in mol2 file
feature
CGQ prompt
CGQ prompt
CGQ prompt
Chain
of atoms
renaming in biopolymers
trace in biopolymers
Change
background
cone
display styles
fonts
iso
molecule
plane
slicing surface positions
volume
molecule name
substructure name
Channel surfaces
batch
creating
theory
tutorial
Charge
computation in a spreadsheet
compute
derivation for biopolymers
display
KOLL_ALLC and KOLL_ALLN
parameters
Del Re
Gasteiger and Marsili
Hückel
remove
undisplay
use in energy calculation
use in torsional minimization calculation
validate
distribution
use in Selector
TAILOR
built-in set
modify
loading in biopolymers
Charge calculation methods
Del Re
Gasteiger-Marsili
references
Gast-Huck
Hückel
references
Pullman
references
Charge derivation for biopolymers
references
CHARLIE
tutorials
bridge generation
scaffold replacement
ChemScore function
Child CSLN
adding to UNITY database
definition
generating
naming
Child SLN
definition
generating
CHIRAL
Chiral acyclic atoms
definition
Chiral atom count
SLN_OPS method
SLN_T method
Chiral atoms
Chiral bridgehead atoms
definition
Chiral built-in set
Chiral protoinvertible atoms and bonds
definition
Chiral ring atoms
definition
Chiral ring fusion atoms
definition
Chirality
flag
specify for atoms
core in Legion
Legion variation list
TAILOR
atom attribute
check
Chirality
invert
select by
specify for atoms
CHORAL
command
examples
format
in the ORCHESTRAR project manager
chorus
Chromosome definitions
Chromosomes
Class
define in a database
Cleanup SPL macro
Clear Model
Clear the screen
Client
command line
Client identification, syb3dbserver
Client-side importing
Clique detection
controlling
CLOGP
background information
column type
definition
error codes
metric in Selector
Close
hitlist
hitlist manager
tps
Close Contact Ratio
Close SYBYL
Closed Connection
tps
Cluster
input molecules
Tuplets
definition
hierarchical
command format
dialogs
theory
tutorial
Jarvis-Patrick
command format
dialog
theory
Reciprocal Nearest Neighbor
command format
theory
Jarvis-Patrick
setting in Selector
theory
Reciprocal Nearest Neighbor
setting in Selector
theory
selecting central compounds
use in Selector
dialog box
theory
viewing and reselecting
rows
Jarvis-Patrick
TAILOR
Reciprocal Nearest Neighbor
TAILOR
TAILOR
CMR
background information
column type
definition
error codes
metric in Selector
CODA
command
examples
format
FRAGDB
build and use personal version
rebuild the main database
FREAD
in the ORCHESTRAR project manager
overview
PETRA
Coefficient plot
Cofactor
adding to biopolymer
database
in the ORCHESTRAR project manager
SYBYL atom types
COLLECT
Collect commands into a file
Collect commands into a file
syb3dbserver
Color
background
dendrogram
ATOM
BOND
By Spectrum
Carbons by Spectrum
Carbons/Hydrogens by Spectrum
color editor
LABEL
SURFACE
TYPE
coding
MOLCAD problem
MOLCAD surfaces
ramps in MOLCAD
TAILOR
dynamic hydrogen bonds
static hydrogen bonds
protein loop
Color Editor
Color ramp
electrostatic potential
electrostatic potential
hydrogen bonding
lipophilic potential
lipophilic potential
local curvature
Color ranges dialog box
Coloring features
Coloring features
Coloring features
Column
adding
copying
deleting
dynamics
expressions
examples
formatting
grid resolution
hiding
modifying
moving
naming
pasting into another spreadsheet
resizing label
resizing width
right-click menu
selecting in table
selecting via the menubar
selection dialog
types
adding
ProTable
AMPAC
adding in SiteID
Column distribution graph
command format
dialog box
protein loop search
theory
Column type
amino acid number
AMPAC
angle
area
array
atom pair fingerprint
atomic coordinates
ClogP
CMR
CoMFA
CoMSIA
conformational angle
conformer
consensus
coordinate map
CPSA
deformation
dictionary angle
dipole moment
distance
distance map
double
double array
energy
EVA
explicit data
family
fingerprint
float
functional data
gridded distance
hologram
integer
inter loop RMS
interesting
kinetic energy
local temperature
molecular weight
MOPAC
neighbors
number of hydrogen bonds
plane angle
plane height
polar surface area
polar volume
QSAR prediction
radius of gyration
range
RMS movements
row number
scale tor
search 2D
search coordinate map
search distance map
secondary structure
sequence homology
sequence number
sidechain probability
similarity
sized array
SLN property
solvation free energy
SPL
strain
string
substituent constant
surface area
TOPCOMFA
Topomer CoMFA
Topomer CoMFA prediction
torsion
transfer free energy
Tuplets similarity
van der Waals contact
vector
vector array
VolSurf
VolSurf prediction
volume
weighted sum
amino acid number
conformational angle
hydrogen bonds
neighbors
secondary structure
sequence number
solvation free energy
solvent accessible surface
surface area
temperature factor
transfer free energy
CoMFA
CoMSIA
EVA
Column types
TOP_PREDICT
CombiFlexX
CScore
TAILOR
analyzing
analyzing results
and Legion
CScore
customizing
FlexXc
graphs
OptiDock
files created
OptiDock glossary
OptiSim parameters
results spreadsheet
setting up
example
theory
tutorials
CombiLibMaker
notes & requirements
troubleshooting
Combinatorial library
definition
prioritize using Tuplets
view Tuplets results
docking
examining
Combinatorial library
building
definition
Combinatorial SLN
building
definition
Combinatorial structure
example
Combine
hitlists
variation sites in Legion
search datasets
Combined searching
CoMFA
column type
field fit consideration
adding column
aligning molecules
alignment rule
conformer column
contouring fields
database align
diagram
dialogs
column definition
region
view CoMFA
view eva
examination of results
field
hints
PLS run
prediction
preparation
probe atom
QSAR optimize
region
region focusing
command format
dialog box
scatter plot
table building
theory
tutorials
introduction
unique compounds
use of results
metric in Selector
auto_region
TAILOR
TAILOR
Command
descriptions
descriptions
UNITY
descriptions
CScore
O/S utilities
Distill
descriptions
HQSAR
O/S utilities
HQSAR
descriptions
license management
tps
descriptions
MOLCAD Plus
descriptions
QSAR
O/S utilities
Selector
expression generators
define
list
macros
activate command set
deactivate command set
define
delete
list
sets, SPL
SPL command
definition
descriptions
trigger execution
O/S utilities
protein database
scripts
UDCIMPORT
UDCSEARCH
Command line
client
Command mode
default values
special characters
Commands
basics list
Confort
Common cores
Common substructure
definition
Common tasks
Common volume overlap
Communication file
create
Compare SLN_Ts
Compare to MOLCAD eps
Compatibility
cross-platform
Compatibility grid, docking functionality
Compatibility grid, docking functionality
Compatibility grid, docking functionality
COMPLEX_PROPERTY
tps
Components
optimal number
Composer
Structurally Variable Regions
using QSAR
Compound-based visualization tools
DiverseSolutions addons
Compound filtering
dbslnfilter
dialog
Compound selection suggestions
Compress domain index
Compressed bitmap
Computing index statistics
CoMSIA
column type
field descriptions
theory
tutorial
viewing results
TAILOR
Concord
3D coordinate generation
Surflex-Dock
O/S utility
notes & requirements
troubleshooting
computation in a spreadsheet
3D building in Selector
3D coordinate generation
FlexS
Surflex-Sim
GUI
how to access
input modes
introduction
licensing
open graphical interface
output
size limits
standalone commands
SYBYL command
concord.pref example file
Cone surfaces
batch
characteristics
coloring
creating
theory
tutorial
Cones
changing attributes
create and display in MOLCAD Plus
in MOLCAD Plus
MOLCAD Plus tutorial
Confidence limits
Configuration
files
Tuplets
tuplets.cfg file
license file
Trigo
Learned Index
Oracle
Confirming predictive power of the model
Conformation
generation
naming conventions
SCAN
valid state names
changing in biopolymers
copying in biopolymers
finding in biopolymers
rotamer libraries
Conformational analysis
background reading
GA conformational search
grid searching
multisearch
random searching
systematic search
Conformational angle
Conformational angle
column type
Conformational states
Conformer
column type
generation
update in DISCOtech
column
dialog box
tutorial
Confort
advanced options
commands
diverse conformer subset generation
exceptions file
final optimization and output options
Generate Conformer Population dialog
geometry optimization
input
intermediate conformer processing
introduction
license requirements
log file
low energy conformer subset generation
modify output details
output
search details
search limits
Single entry point energy calculation
Tripos Force Field
Confort and FlexS
Confort and FlexX
Confort command control files
Confort in SYBYL
Confort sessions
custom defaults
Confort Sessions Menu
Conjugate gradient method
Connect to server from SYBYL
CONNECT, tailor variable
Connection Bond
Connection flag
Connection table
Connection table
Connection table
Connection tables
Connectivity
quick bonds
quick bonds
search
CONNOLLY
scaling factor
SURFACE
surface
Consensus
and best consensus
column type
scoring
definition
introduction
selecting the best docked solution
within a spreadsheet
Consistency
chemical structure
Constraining distances
Constraint
Bond Path
Constraint violations
Constraints
bond path
normal
angle
between lines and planes
dihedral angle
distance
partial match
partial match
spatial
spatial cap
spatial line
spatial plane
spatial point
torus
volume
containing
exclusion
receptor cavity
receptor site
surface
set tolerance
description file
angle
define
list
modify
remove
dialog description
distance
define
list
modify
remove
multifit
define
list
range
define
list
modify
remove
torsion
define
list
modify
remove
viewing
set tolerance
add/modify
and flexible rings
set tolerance
bond path
normal
angle
between lines and planes
dihedral angle
distance
partial match
spatial
spatial cap
spatial line
spatial plane
spatial point
torus
volume
containing
exclusion
receptor cavity
receptor site
surface
constraints2stream
Containing constraints
receptor cavity
receptor cavity
Continuous Drawing Mode
Cancel point of attachment
CONTOUR
ANALYZE
ASCII_CONV
DISPLAY
header information
CoMFA fields
details
specifications
TAILOR
analyze
TAILOR HISTOGRAM
Contour files
creating
creating coulomb ESP
creating in batch
creating poisson-Boltzmann contour
creating with MOLCAD Plus
MOLCAD Plus
creating contour files
electron density
isopotential
MVOLUME
MO plot
Contour graph
isocontour
QSAR
Contributions
dialog
graphs
Convert
files (sln2img)
MDL molfile to SLN
screens
SLN to MDL MOL file
SLN to SMILES
SLN to SYBYL MOL2 file
SMILES to SLN
SYBYL MOL2 file to SLN
table formats
table formats
Convert old domain index
Cooman plot
COORDID_SEQUENCE
Coordinate
attributes
generate 2D
object type
Coordinate map
dialog box
search setup
Coordinates
duplication check
generate 2D
list
MODIFY
COORD_T type
Copy
molecule area contents
Core
definition
Core File Identifiers
Core placements
definition
Core structure, definition
Core structure, definition
Cosine
Cosine coefficient in Selector
Cost definition
Coulomb
creating contour files
Counterion table
counterion.defs
Coverage Flag Attribute
Covering atoms
Covering atoms
Covering atoms
CPK
CPSA
columns
tutorial
TAILOR
CRC calculation
Create
hypothesis
query
Tuplets
tuplets
Create fingerprint domain index
Create registrar
Create SLN domain index
from fingerprint set
Create UNITY query
from a ligand
create_dataset
Creating
database
dialog description
hypothesis
from molecule
from UNITY query
Tuplets
DISCOtech run
active site
CDF file
EDF file
RDF file
SFXC file
family
generalized surfaces
3D volume
contour files
density & electrostatic potential contour files
density contour file dialog
electron density slicing plane
electrostatic potential contour files
electrostatic potential iso surfaces
electrostatic potential slicing plane
esp contour file dialog
esp surface contour file dialog
interactive cones
interactive iso surfaces
iso surfaces
separating surface
separating surfaces
slicing plane
command sets
expression generators
definition
macros
scenes
variables
associative arrays
built-in
core file
defined arrays
user defined
small molecules
biopolymers
unit cell box
Credentials
tps
Credits
Crippen parameter tables
Cross-platform compatibility
Crossover
operator
Crossvalidation
diagram
group membership
negative values
number of groups
prediction
theory
with PLS
CRYSIN
data record
TAILOR
transformation matrix
tutorial
Crystal
add single bonds
classes
connect atoms
create box
delete box
expand cells
file formats
list molecule information
load coordinates
modify atom parameters
remove molecule definition items
save to ASCII file
space group
data files
tables
specify symmetry
specify unit cell parameters
transformation operations
Crystallographic data
CScore
best solution
bibliography
ChemScore
command outside SYBYL
command within SYBYL
consensus and best consensus
consensus definition
D score
details
extraction
F Score
FlexX-Pharm Constraints
G Score
graphical user interface
introduction
menu
O/S utility
operation mode
parameters
PMF score
purpose
requirements
running in CombiFlexX
running while docking
selecting the scoring functions
subset extraction
theory
tutorials
using within a spreadsheet
working with metal atoms
TAILOR
files created
running in CombiFlexX
CSLN
building
child
adding to UNITY database
generating
naming
definition
definition
enumerating
enumerating
exploding
naming
parent
retrieval
CT
CT
CT
Ct Attributes
Cubic system
Current conformation
Curvature column
Customization of
RDF file
Customize
start up
SYBYL startup
texport size
Customize Concord defaults
Customize Confort
sessions
Customize StereoPlex
sessions
Customizing SYBYL
during execution
environment variables
TA_COLORMAP
TA_COLTYPES
TA_DISPLAY_CONFIG
TA_MENDYL_TAILVALS
TA_SYSTEM_STRT
TA_USER_STRT
XUSERFILESEARCHPATH
example .sybylrc file
menubar
adding new pull-downs
adding new pull-downs to spreadsheet
adding options to existing pull-downs
adding options to existing spreadsheet pull-downs
predefined variables
OTHER_DIRECTORIES
SYBYL_MENUBAR_ADDONS
TA_MENUBAR_USER_INIT
TA_MSS_USER_INIT
SPL column types
X Resources
.Xdefaults file
Sybyl file location
Cyclic peptide
Cylinder options


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




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