Chapter 5: Building and Adjusting Structures
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When you click the last atom, the distance is highlighted with two yellow solid lines, a
purple dotted line, and an arrow indicating the direction of adjustment. Angles are high-
lighted in green and orange, and dihedrals are highlighted in red and turquoise.
3. With the left mouse button, drag to the right to increase the distance or to the left to
decrease it. Alternatively, use the scroll wheel or the pinch gesture to adjust the distance.
You can choose bond lengths or dihedrals for adjustment by right-clicking on a bond in the
Workspace and choosing
Distance
or
Dihedral
from the
Adjust
submenu on the shortcut menu.
For a faster adjustment of a dihedral, choose
Quick Torsion
from the
Adjust
button menu, click
on a bond, then drag with the left mouse button. The fragment that is rotated has an arrow
pointing to it on the end of the bond nearest the moving fragment. By default the smaller frag-
ment is rotated around the selected bond. To change the fragment that is rotated, click the bond
again.
Quick Torsion
is selected by default, so if you have not previously selected some other
adjustment, you only need to click on the
Adjust
button, then perform the adjustment.
If you want to display interactions such as hydrogen bonds and contacts while adjusting struc-
tures, you can select
Display Interactions
from the
Adjust
button menu. The interactions that are
displayed can be set as preferences—see
Section 14.8.2 on page 365
for more information.
5.9.1.2
From the Adjust Panel
The tools for adjusting bond lengths, bond angles, and dihedral angles are similar, so the
description given here is generic.
Figure 5.7. The Adjust panel, showing the Dihedral tab.
Chapter 5: Building and Adjusting Structures
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To define the geometric parameter that you want to adjust, choose
Atoms
or
Bonds
from the
Pick
option menu in the
Define atoms for
operation section, and pick the atoms or bonds. For a
bond length, you must pick two atoms or one bond; for a bond angle, you must pick three
atoms or two bonds; for a dihedral angle you must pick four atoms or one bond—the bond
about which the rotation is performed. When you pick this bond, the groups attached to the
atom nearest the point you click are the ones that are moved.
In addition to the standard picking tools just described, you can also specify dihedrals in
proteins using standard names (psi, phi, omega, etc.). Click
Select
in the
Dihedral
tab and
select dihedrals by the residues in each entry (or chain), or by standard names.
The atom numbers of the selected atoms are listed in the table in the center of the tab. The last
atom that you pick is the “target atom”—the atom that is moved in the adjustment process. You
must also decide which of the attached atoms to move along with the target atom. You can
choose from
All attached atoms
,
All attached terminal atoms
, or
Only single atom
. If the target
atom is part of a ring, the first option is unavailable.
Once you have chosen the atoms for a particular adjustment, you can make the adjustment by
dragging with the left mouse button, by using the scroll wheel, or by entering a new value for
the geometric parameter in the
Current
column of the table. If you enter a new value, the value
is changed and the Workspace is updated when you press
ENTER
. You can make adjustments
using the table at any time, but you can only use the mouse immediately after picking.
5.9.1.3
Repeating Adjustments
When adjusting a structure, you might want to switch between adjusting two or more parame-
ters. If the parameters are of the same type, you can select the previous or the next adjustment
by choosing
Edit
→
Adjust
→
Previous Adjustment
or
Edit
→
Adjust
→
Next Adjustment
, or use
CTRL+SHIFT+A
(
Z
) and
CTRL+SHIFT+Z
(
Z
). If they are of different types, you can
select the adjustment type again, using the
Edit
menu or the
Adjust
button,
and the last adjust-
ment of that type made is selected. You can also select the adjustment you want to change in
the
Adjust
panel, by selecting the table row in the tab for the adjustment type.
5.9.2
Adjusting Peptide Linkages and Side Chains
The
Adjust
button menu on the main toolbar provides some tools for adjusting the geometry of
peptide linkages, and for selecting the most common rotamers for side chains.
For peptide linkages, you can rotate the plane of the peptide linkage, rotate the carbonyl plane,
and convert between cis and trans linkages.