Correcting Water Orientations
If the orientation of water molecules is incorrect, reorient the molecules with the following procedure:
|
1.
|
Pick the water molecule in the Workspace. |
|
2.
|
In the 3D Builder panel, click Move . |
The Move Atoms banner is displayed, giving instructions.
|
3.
|
Middle-click the oxygen atom. |
This ensures that the rotation is about the oxygen atom, rather than about the centroid of the water molecule atoms, which will shift the oxygen as well as the hydrogens.
|
4.
|
Use the middle mouse button to change the orientation of the water hydrogens. |
|
5.
|
Pick another water molecule and repeat the above two steps. |
|
6.
|
Dismiss the Move Atoms banner. |
You might also have to adjust the geometry of some groups in the active site. Check particularly for GLN and ASN: the N and O atoms can look the same in the X-ray structure determination, so they might need to be flipped at their terminal dihedral if there is a poor hydrogen-bonding pattern or steric clashes. Likewise, the ring in HIS might need to be flipped. You can do this by rotating the dihedral angle by 180°.
To rotate a dihedral angle:
|
1.
|
Right-click the bond around which you want to rotate, and choose Rotate Dihedral. |
An arrowhead is placed on the bond, pointing to the group that will be rotated. If this is not the correct group, click on the bond again.
|
2.
|
Use the mouse wheel or drag horizontally (with the left mouse button) to change the angle. |
If you want to be more precise in the rotation, use the following steps:
|
1.
|
ChooseInin the Maestro main window, choose Edit → Adjust → Angles / Dihedrals. |
|
2.
|
Pick four atoms to define the dihedral angle. |
The fourth atom should be one of the atoms in the group you want to rotate. Markers and the value of the angle are displayed.
|
3.
|
Drag horizontally with the left mouse button or scroll with the mouse wheel until the angle has changed to the appropriate value. |