Prime User Manual - ISP

10
Chapter 2: Using Prime–Structure Prediction
2.3.2 The Edit Menu
The Edit menu contains commands for editing sequences and secondary structure predictions.
These editing tools are also available from the Prime toolbar, and are described with the
toolbar in Section 2.4 on page 13.
2.3.3 The Display Menu
The Display menu includes the following commands for controlling the appearance of the
sequence viewer and structures in the Maestro Workspace.
Color Scheme
This command opens a menu of coloring options. In Prime–SP, the coloring schemes act as
modes; that is, only one color scheme can be used at any given time. Each step in Prime has a
default color scheme. You can use this menu to choose a different one. When amino acid
sequences are added to the sequence viewer, they are colored according to the scheme that is
currently selected.
When the structure associated with a sequence is displayed in the Workspace, it is generally
colored using the same scheme as the sequence. However, protein structures in the Workspace
are sometimes colored using other color schemes:
• When a PDB structure is imported, it is displayed in the Workspace using an error reporting
color scheme in which complete recognized residues are gray, incomplete residues
are red, unknown or nonstandard residues are orange, residues with multiple location
indicators are green, and recognized residues with some unrecognized atoms are blue.
For more information about conversion of PDB structures, see the Maestro User Manual.
• When the Build Structure step is complete, the color scheme applied to the structure in
the Workspace is Atom PDB B Factor (Temperature Factor), in which blue atoms are those
derived directly from the template, and red atoms have been predicted or modeled. To
restore this color scheme, choose Atom PDB B Factor (Temperature Factor) from the
Color all atoms by scheme Maestro toolbar button.
The Prime color schemes are:
• None: All sequences are colored standard gray.
• Color by Sequence: The query sequence is colored standard gray. Each of the other
sequences uses a different color.
Prime 2.1 User Manual