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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.
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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
).
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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.