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The set of fragment buttons on the
Fragments
toolbar provides a limited selection of structural
fragments. These fragments can be added to the Workspace in Place mode (see
Section 5.3.1
on page 84
for details). The intention is that you build with these fragments to create the basic
molecular framework, then change the element to introduce heteroatoms. A few specialized
fragments with heteroatoms are provided, such as a planar amine fragment, which is useful for
building amides. The fragment names are displayed in tool tips. A much larger set of fragments
is available from the
Build
panel, which you can open by clicking the
Fragments
button:
The ring fragments can be attached by connection to an atom, which you do by picking an
atom, or by fusion with a bond, which you do by picking a bond. The picking cursor is labeled
A|B
to indicate that either an atom or a bond must be picked.
Decrement bond order
Decrement the order of the bonds you pick in the Workspace by one, to a minimum of 0. Zero-
order bonds are displayed with dashed lines (or tube segments).
Increment formal charge
Increment the formal charge of the atoms you pick in the Workspace by one unit.
Decrement formal charge
Decrement the formal charge of the atoms you pick in the Workspace by one unit.
Invert chirality or flip ring substituents
Invert the chirality at a chiral center, or swap the substituents on an aliphatic ring atom, by
picking the chiral center or the ring atom. Double-click to invert the chirality of all atoms.
Move
Choose a direction for moving atoms, then click the atom to be moved. Moves in the XY plane
are made by clicking the new location. Moves in the Z direction are made in 0.5 Å increments.
Clean up geometry
Cleans up the geometry of the structure or the selected atoms in the Workspace by performing
a short force-field minimization.You can choose the minimizer from the button menu:
Built-in
for the built-in minimizer using the OPLS_2005 force field, and
UFF
for the universal force
field minimizer, which covers more elements.
Sculpt
Select and move atoms, followed by a short force-field minimization of the atoms in the same
residue (or molecule). Atoms in residues within 5 Å are constrained, and the rest are frozen.
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In addition to the organic fragments, there is a button for placing metal centers, from which
you can choose a metal center type, and place it in the Workspace.
The metal centers are also available in the
Build
panel. Once a metal center is placed, you must
set the element for the metal center, as the metal is undefined (a dummy atom). By default, the
attached ligand at each coordination site is hydrogen, but you can change it or replace it with a
fragment or a metal ligand.
5.2
The Build Panel
The
Build
panel consists of three tabs. The primary building tools are contained in the
Frag-
ments
tab. The
Fragments
tab contains several fragment libraries from which you can select a
fragment and add it to the Workspace, either by positioning it manually or by using predefined
grow rules. The other two tabs,
Atom Properties
and
Residue Properties
, contain tools for
changing the properties of atoms or residues. The use of these tabs is described in the following
sections.
To open the
Build
panel with a particular tab displayed, choose
Edit
→
Build
→ tab, or choose
the tab from the
Build
toolbar button menu on the
Edit
toolbar (if shown).
You can also open the
Build
panel at the
Fragments
tab with the
Fragments
button on the
Frag-
ments
toolbar.
Hydroxyl
Methyl Cyclobutadienyl
Planar amine
Cyclopropyl Phenyl
Sulfonyl Cyclobutyl
Cycloheptyl
Carbonyl Cyclopentyl
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5.3
Building a Structure From Fragments
Whenever possible, you should use fragments to build structures. Building from fragments
ensures the correct geometry within each fragment, and thereby reduces the work needed to
minimize the structure. In addition to the small set of fragments on the Fragments toolbar, the
following fragment libraries are available in the
Fragments
tab of the
Build
panel:
Figure 5.1. The Fragments tab of the Build panel, showing the Organic library.
• Organic
• Amino acids
• Rings
• Nonstandard
amino acids
• N-heterocycles
• Modified amino acids
• O-heterocycles
• Protein capping groups
• S-heterocycles
• Protein ions & solvents
• Mixed heterocycles
• Deoxyribonucleic acids
• Carbohydrate furanose
• Ribonucleic acids
• Carbohydrate pyranose
• Double-stranded A DNA
• L carbohydrate furanose
• Double-stranded B DNA
• L carbohydrate pyranose
• Double-stranded A RNA
• Metal centers
• Double-stranded B RNA
• Metal ligands
• Diverse fragments