Maestro User Manual

Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

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When you change the bond order, the valence states of the atoms can be violated. Maestro

gives no warning of this violation, so it is up to you to ensure that your structure is valid.

• To increase the formal charge, click the 

+ Formal Chg

 toolbar button

then click the atoms whose formal charge you want to increase. You can only increase the

formal charge one atom at a time. However, the formal charge is also set when you

change the MacroModel atom type.

• To decrease the formal charge, click the 

- Formal Chg

 toolbar button

then click the atoms whose formal charge you want to decrease. Like increasing the for-

mal charge, you can only decrease the formal charge one atom at a time, and the formal

charge is set when you change the MacroModel atom type.

5.8

Connecting or Fusing Structures

To build some structures, it is sometimes convenient to connect or to fuse two existing struc-

tures. Connecting two structures creates a new bond between two selected atoms, with deletion

of appropriate hydrogens. An example is the creation of bipyridyl from two pyridine rings, by

connecting the 2-carbon on one ring with the 5-carbon on the other, and deleting the hydrogen

atoms. Fusing two structures deletes atoms. An example is the fusion of two benzene rings, in

which two carbon and two hydrogen atoms are deleted from one ring, and bonds formed to the

other ring with deletion of two hydrogen atoms, to form naphthalene.

Fusion of rings can be accomplished when building structures using the 

Build

 toolbar. Each

ring fragment can be fused onto the existing structure by clicking a bond. 

You can connect structures with draw mode, by clicking on the two atoms you want to connect.

However, no adjustment of the geometry is made when you do so.

More general tools for fusing and connecting structures are available from the 

Connect and

Fuse

 panel, which you open from the 

Edit

 menu. The panel is docked into the Workspace by

default, but you can move it out. In the connection and fusion operations, an attempt is made to

create structures with reasonable geometries, and a check is made that valency is not violated.

This is in contrast to Draw

 

mode, which does not evaluate bonding or geometry. 

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Figure 5.6. The Connect & Fuse panel.

For both connect and fuse operations, you must first select atom pairs to be joined. The atoms

you select must not be hydrogen atoms. You can select as many pairs as you like. The first

atoms in all selected pairs must all come from the same molecule, and the second atoms in the

pairs must come from the same molecule. The molecule for the set of first atoms set need not

be different from the molecule for the set of second atoms. If you select a pair of atoms in the

same molecule, a new bond is drawn between the atoms.

To select atoms for a connect or fuse operation, ensure that 

Pick to define atom pairs

 is selected

and click on the Workspace atoms to define the pairs. Atom numbers of the selected pairs

appear in the 

Connect or fuse atoms

 list. Also, if 

Show Markers

 is selected, each pair is marked

with a dashed green line. For the pair that is selected in the list, the green line is flanked by

solid yellow lines. The lines disappear once the connect or fuse operation is completed.

When fusing structures, the order in which you select the atom pair is important. The first atom

selected is replaced by the second atom selected. For example, when fusing an amino nitrogen

and an ethyl carbon, selecting the nitrogen first results in its deletion, followed by attachment

of the remaining atoms of the amine to the ethyl carbon. Selecting the ethyl carbon first results

in deletion of the carbon and retention of the nitrogen.

To delete an atom pair from the 

Connect or Fuse Atoms

 list, select the pair in the list and then

click 

Delete

. To clear the atom pair list, click 

Delete All

.

When you have selected all the pairs of atoms that you want to connect or fuse, click the appro-

priate button—

Connect

 or 

Fuse

.

If you are performing a connection or fusion between structures belonging to different project

entries (the source entries), the result must belong to a single entry. When you click 

Connect

 or

Fuse

, the 

Choose Entry

 dialog box opens, and you must specify the entry with which the new

structure should be associated. Subsequent actions depend on which entry you choose:

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• If you choose one of the two source entries, the other entry is deleted.

• If you choose an existing entry other than the two source entries, the new structure is

added to the existing entry and the source entries are deleted.

When you draw a bond between two entries, a new entry is created automatically, and you can

name the new entry in the 

Create Bond

 dialog box. If one of the entries is a scratch entry and

the other is a project entry, the scratch entry atoms are added to the project entry and the

scratch entry is deleted. If both entries are scratch entries, they are merged into one of the

scratch entries and the other is deleted. 

You can undo a connect or fuse operation, and the changes to the entries are also undone. 

5.9

Adjusting the Geometry

Before you use a structure for a calculation, you might want to adjust the geometry, especially

if you used Draw mode, or if the Grow mode orientation was incorrect. Maestro provides tools

on the 

Edit

 toolbar for the most common adjustments, on the 

Adjust

 button menu. 

More flexibility is provided in the 

Adjust

 panel, which you open from the 

Adjust

 submenu of

the 

Edit

 menu in the main window. The tools that are available on the 

Adjust

 button menu are

also available from the 

Adjust

 submenu of the 

Edit

 menu.

5.9.1

Adjusting Distances, Angles, and Dihedral Angles

You can change distances, angles, and dihedral angles, either directly in the Workspace or by

using the tools in the 

Adjust

 panel, as described below. If you are making a sequence of adjust-

ments of the same type, you can easily recall the previous or next adjustment. 

5.9.1.1

Using the Workspace Tools

The basic process for adjusting parameters directly in the Workspace is the same for distances,

angles, dihedral angles, and chirality. This description uses distances as an example:

1. Choose 

Distance

 from the 

Adjust 

button menu on the 

Edit

 toolbar:

2. In the Workspace, click on two atoms to define the distance.

A purple cube is drawn around the first atom, to indicate that it has been selected. For

angles and dihedrals, a cube is drawn around each subsequent atom.

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