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Chapter 5: Building and Adjusting Structures

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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

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