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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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