Prime User Manual - ISP

8
Chapter 2: Using Prime–Structure Prediction
In the upper part of the panel is the Prime menu bar, and below that is the Prime toolbar. Below
the Prime toolbar is the Prime sequence viewer. You can resize the sequence viewer by dragging
the small box in the right-hand corner of the horizontal line that separates the sequence
viewer from the main panel. You can select a single residue in a sequence by clicking on it, and
you can select multiple residues using shift-click to select a range and control-click to select or
deselect individual residues.
In addition to displaying sequences for the query and for templates, in some steps the sequence
viewer shows secondary structure predictions (SSPs). Right-click on an SSP for a menu of
commands that includes Hide All, Delete, and Export. Right-clicking on a sequence also
produces a shortcut menu of commands appropriate to the current step. You can export
sequences using the Export Sequences command on the Prime File menu.
The sequence viewer includes a “ruler”, which marks the residue position relative to the leftmost
residue displayed in the sequence viewer. This residue position is displayed in parentheses
in the tooltip for each residue. The positions are arbitrary, and can change when you
display residues in the viewer. They are intended to help you keep track of the sequence as you
scroll the sequence viewer.
The sequence viewer can be configured to display a single line for the sequence that can be
scrolled horizontally, or the sequence can be wrapped so that it scrolls vertically. The configuration
is controlled by the Wrap Sequences option on the sequence viewer shortcut menu.
If you want to save an image of the sequence viewer, choose Save Image from the sequence
viewer shortcut menu. A file selector opens, in which you can select a format, from PNG,
TIFF, and JPEG, and save the image.
Below the sequence viewer are the step name and a brief description of the step, followed by a
row of buttons. The first button on the left runs the main action of the step, which may involve
launching a job. See Section 2.5 on page 14 for more information on running Prime jobs. An
Options button is usually located to the right of the action buttons. Most buttons, including
those in the Prime toolbar, the Prime Guide, and the Maestro toolbar, have tooltips that you can
view by pausing the cursor over the button.
The job status icon in the upper right corner of the panel turns green and spins when you
launch a job. When the icon turns pink again, the job is finished. Click the icon to open the
Monitor panel. For more information on job control, see Section 2.5 on page 14.
The center of the panel contains the Step View, which shows data relevant to the step in table
format. In the Build Structure step, the Step View contains output from the Build Structure
job’s log file. You can view the complete text of a truncated table entry as a tooltip by pausing
the cursor over the text. To resize a table column, drag a column border using the middle
mouse button. You can sort the tables in the Step View by clicking the column heading, once
Prime 2.1 User Manual