Maestro User Manual

Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

102

To perform peptide rotations:

1. Choose 

Rotate Peptide Plane

 or 

Rotate Carbonyl Plane

 from the 

Adjust

 button menu on

the 

Edit

 toolbar.

2. Click on an atom in the peptide group to select it.

The peptide group is marked with a rectangle.

3. Drag with the left mouse button to perform the rotation.

To convert between cis and trans:

1. Choose 

Convert Cis/Trans

 from the 

Adjust

 button menu on the 

Edit

 toolbar.

2. Click on one of the atoms in the peptide link. 

The geometry of the converted link is only approximate, and should be refined before use in

any application that depends on the accuracy of the geometry. 

To select a rotamer for one or more residue side chains:

1. Select the residues in the Workspace or the sequence viewer. 

2. Choose 

Rotamers

 from the 

Adjust

 button menu on the main toolbar.

The 

Rotamers

 dialog box opens. This dialog box has a list of the residues you selected in

the Workspace at the top and a list of rotamers for the residue that is selected from this list

below, with angles and a standard percentage population for each rotamer.

3. Select a residue from the table at the top of the dialog box.

The residue is highlighted in the table. The Workspace view zooms to that residue if 

Fit

selected residue to Workspace

 is selected.

4. Select a rotamer from the lower table. 

The side chain is rotated to the geometry of the selected rotamer. You can sort this table

by clicking on the column headings. 

Repeat steps 

3

 and 

4

 for each residue that you want to adjust. Note that no account is taken of

steric clashes when selecting rotamers; however the presence of clashes is indicated by a + sign

in the 

Clash

 column. If you decide that you prefer the original rotamer, you can select it in the

table or click 

Restore to Original Conformation

. 

When using PrimeX, further options are available—see 

page 16

 of the PrimeX User Manual.

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Chapter 5: Building and Adjusting Structures

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Figure 5.8. The Rotamers dialog box.

5.9.3

Adjusting the Stereochemistry

The simplest way of adjusting the stereochemistry at a chiral center is to use the toolbar button,

To invert the chirality, click this button, then pick the chiral center in the Workspace. The

groups to move are automatically selected, as the lowest-priority groups. You can also use this

button to exchange substituents on a single atom of an aliphatic ring. To invert the chirality at

all chiral centers, double-click this button. The structure is reflected in the xy plane to produce

its mirror image. This procedure can be used for any structure, including fused rings.

If you want more flexibility, you can use the picking tools in the 

Chirality

 tab of the 

Adjust

panel. You can invert the chirality of selected chiral centers or of all chiral centers. This tab

also has buttons for displaying the R and S labels for the configuration at chiral centers, and for

clearing the labels. If you click 

Label Chiral Centers

, all other labels are cleared.

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Chapter 5: Building and Adjusting Structures

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To invert the chirality at a given chiral center, select the chiral atom, then select the two other

atoms that are connected to the chiral center that are to remain in place. After you have picked

the third atom, the two atoms that were not picked are interchanged, with their attached groups.

You can also choose 

Chirality

 from the 

Adjust

 button menu on the 

Edit

 toolbar, and select atoms

as described above.

To invert the chirality at all chiral centers, click 

All

 in the 

Invert chirality

 picking tools section.

These procedures do not apply to changing the chirality of atoms in fused ring systems at the

intersection of the rings, for which the chiralities of several centers are usually related in a low-

energy structure. 

To adjust the stereochemistry around a double bond (cis-trans isomers), choose 

Convert Cis/

Trans

 from the 

Adjust

 button menu, then click on a double bond. A rotation of 180º around the

double bond is performed, by adjusting the end that has the smallest number of attached atoms.

This is the same tool as for adjusting peptide linkages, but with a different target. 

5.9.4

Adjusting Groups of Atoms

Sometimes, you might want to adjust the position of a more general group of atoms—for

example, you might want to adjust the position of a ligand with respect to a receptor, or you

might want to move a functional group from one part of a molecule to another, by breaking the

bonds and re-attaching it in its new location. You can do this with the local transformation

tools, which are available from the 

Transform

 submenu of the 

Edit

 menu, the 

Advanced Trans-

formations

 panel, and the 

Transform 

button menu on the 

Edit

 toolbar.

To open the 

Advanced Transformations

 panel, choose 

Edit 

→

 Transform 

→

 Advanced

, or

choose 

Advanced

 from the 

Transform

 button menu.

A local transformation is just like a global transformation (change of view), except that you are

moving an atom subset

1

 with respect to the other atoms in the Workspace. Local transforma-

tions use the same keyboard and mouse actions as global transformations.

1.

The subset can in fact include all atoms in the Workspace, so that the rotation or translation actually changes the

coordinates of the entire contents of the Workspace.

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