Maestro User Manual

Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

85

You can build a single structure from multiple fragments in Place mode. Once you have placed

the first fragment, you can join a second fragment to it by selecting the fragment and clicking

in the Workspace on the atom that you want the new fragment to replace. If you click on a

terminal atom, the fragment replaces the terminal atom. If you click on a non-terminal atom,

that atom and its attached hydrogen atoms are replaced by the new fragment. For example,

clicking on a secondary amine nitrogen with a methyl fragment gives a disubstituted methyl

center, and clicking on a disubstituted methyl carbon with an amine fragment produces a

secondary amine center. 

If you are using the build toolbar to add a ring to a structure, you must ensure that you are in

connection mode (

A

 cursor label) rather than fusion mode (

B

 cursor label). Clicking on the ring

button switches between the modes. 

You can also mutate one residue into another in a protein. When you select 

Amino acids 

or

Modified amino acids

 from the 

Fragments

 menu in the 

Build

 panel, a 

Mutate

 button appears

beside the 

Define grow bond

 picking tools. To mutate a residue, select 

Mutate

, select the new

residue from the list and pick an atom in the residue you want to mutate. The new residue

replaces the old residue. A quicker way of mutating a residue is to right-click on an atom in the

residue and choose the new residue from the 

Mutate Residue

 submenu of the shortcut menu

that is displayed.

Figure 5.2. The Fragments tab of the Build panel, showing the Mutate option.

---

Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

86

5.3.2

Building Structures Using Grow Mode

In Grow mode you can take advantage of the predefined “grow” rules that dictate where and

how fragments are connected to build structures. To enter Grow mode, select 

Grow

 in the 

Frag-

ments

 tab of the 

Build

 panel. This mode is only available from the 

Build

 panel.

To create a structure in Grow mode, click the fragments in the fragment library that you want

to assemble in the Workspace. At each click, the selected fragment is added to the structure,

and a green arrow marks the location of the grow bond—the bond that will be replaced when

the next fragment is added.

To grow a structure from a location other than that indicated by the current grow bond, you can

choose a new grow bond using one of the following methods:

• Choose 

Atom

 from the 

Pick

 option menu of the 

Define Grow Bond

 section, and pick two

atoms in the order that defines the grow direction.

• Choose 

Bond

 from the 

Pick

 option menu of the 

Define Grow Bond

 section, and pick a

bond. The grow direction arrow points to the atom closest to where you click.

• Choose 

backward

 from the 

Grow Direction

 option menu. The grow bond moves to the

opposite end of the molecule.

In addition to the fragments, the 

Fragments

 tab of the 

Build

 panel contains controls for setting

the joining geometry, and, where applicable, secondary structure and helix geometry. The

Joining Geometry

 option menu provides context-sensitive options for attaching new fragments

to the existing structure. For example, under the 

Deoxyribonucleic acid 

fragment type, the

joining geometry options are 

Standard Helix

 and 

User Defined

. 

If you choose to define your own joining geometry, you must specify values for the torsions

that define applicable secondary and tertiary structures. When you select the 

User Defined

option and click on the name of the fragment, a dialog box prompting you to enter the angle

value is displayed.

If you are growing a structure with amino acid fragments, and you choose 

user defined

 from

the 

Secondary structure

 option menu, you are prompted for the phi angle and then the psi

angle. When growing in the N

→C direction, the phi angle is applied to the new residue, but the

psi angle is applied to the residue that the new residue is attached to. This is because the N–C

bond is replaced when you grow the next residue; the new residue always has psi set to 180°.

By default, Maestro automatically fits the structure to the Workspace after each grow opera-

tion. You can turn this behavior off in the 

Builder

 tab of the 

Preferences

 panel (see

Section 14.12 on page 371

). 

---

Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

87

When growing residues (amino acids, DNA/RNA, sugars—any fragment that has a residue

name), the residue number is incremented or decremented from the number of the residue that

you grow from, depending on the direction of growth, and the new residue is assigned the same

chain name. For other fragments (that don’t have a residue name), the added fragment inherits

the chain name and residue number of the residue it was attached to by the grow operation. 

5.4

Building a Structure From Atoms

The Build toolbar contains tools for drawing structures in the Workspace atom by atom (Draw

mode), and the 

Atom Properties

 tab and the toolbar contain tools for retyping atoms within a

structure. Maestro does not automatically correct geometries of structures created in Draw

mode. You can adjust the geometry after building the structure from the 

Adjust

 panel. You

should also minimize the energy of the completed structure.

When using Draw

 

mode to create a structure, only a few elements—H, C, N, O, P, S, Si, Al, Cl,

and F—are available by default on the button menu. You can use other elements by choosing

Other

 from the button menu and selecting the element from the periodic table in the element

selector that opens. 

Figure 5.3. The element selector.

Alternatively, you can use one of the common elements to draw the structure, and then change

the desired atoms—see 

Section 5.6

. Maestro allows you to violate the valency of an atom in

Draw mode so that you can change it to an atom of some other element.

The basic operations of Draw mode are described below.

---