Index

add_b script

ASSUME statement

Atom type

ATOMx statement

example of

B

validation

B correlation

Bond angle

Bond length

Break

Break

example of

Bsol

validation

C-terminus

break

normal

CELL statement

CHAIN statement

example of , ,

usage

Chirality

cleanup command

CLUSTER statement

CLUSTER statement

example

defining transformations

entire chains

residue ranges ,

COMBINE statement

command

cleanup

correct

diffcor

diffplot

dscreen

from_pdb

gather

geometry

histogram

hkl_segregate

make_maps

ncs

pekpik

report_hkl

rfactor

scatter

tnt

to_pdb

CONSTANT statement

correct command

Crosslinks

defining a ,

Cystine bridge

defining a ,

diffcor command

diffplot command

Disorder

atomic

molecular

Disulfide bond

defining a ,

DNA geometry definition

dscreen command

Engh & Huber Parameters

EXCLUDE statement

Fixing parameters

FO statement

Free R

from_pdb command

gather command

geometry command

GEOMETRY Statement

detailed discussion

histogram command

hkl_segregate

usage

hkl_segregate command

HKL file

creating

Ideal geometry

definition of

K

Ksol

validation

Limiting parameters

Linking residues

to symmetry images

within a chain

LINK statement

make_maps command

Metal atoms

Molecular disorder

Moses option

Multiple conformations

ncs command

Noncrystallographic symmetry

Noncrystallographic symmetry

constraints

restraints

structural correspondences

OPTION statement

PDB Format

pekpik command

Peptide bond

defining a

example of

Planarity

Pseudorotation angle

r-free script

RANGE statement

report_hkl command

RESIDUE statement

example of ,

usage

RESOLUTION statement

rfactor command

R free

Rigid-body refinement

Rigid bodies and solvent

RNA geometry definition

Scaling Fo's and Fc's

B

Bsol

K

Ksol

scatter command

script

add_b

r-free

tnt_cycle_cons_ncs

tnt_cycle_ncs

SET statement

SET statement

usage

Solvent

in rigid bodies

Special positions

Standard geometry

definition of

finding values for

libraries

Static disorder

Steepest Descent

tnt_cycle_cons_ncs

tnt_cycle_ncs

tnt command

to_pdb command

Torsion angle

TRANSFORMATION statement

example

Trigonal planarity

Weights

Starting guess

WEIGHT statement

Wilson B