Prime User Manual - ISP

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Chapter 2: Using Prime–Structure Prediction
Add Anchors (Edit menu): Set alignment constraints by setting anchors at residue
positions. To remove anchors, click on the same residue again.
Lock Gaps (Edit menu): To prevent gaps from being collapsed during manual
editing, lock the gaps using this button. Locked gaps are indicated with a - symbol.
Unlock Gaps (Edit menu) To allow gaps to collapse during manual editing, unlock
the gaps using this button. Unlocked gaps are indicated with a ~ symbol.
Color Scheme (Display menu): Select a color scheme for coloring sequences in the
sequence viewer. If there is a structure in the 3D Workspace associated with the
sequence, it will also be colored.
View Structure (Display menu): Use this button to display and undisplay structures
in the Workspace.
View SSA (Display menu): Use this button to turn the secondary structure assignment
(SSA) in the sequence viewer on and off.
2.5 Prime Job Options and Control
Before launching a Prime calculation from a step panel, you may want to choose which
machine host the job will run on and check or modify job settings. When a run is complete,
you can incorporate the results into the Maestro Project Table and save them as a project.
2.5.1 The Job Options Dialog Box
The Structure Prediction–Job Options dialog box, shown in Figure 2.2, allows you to specify
which machine each type of Prime job will run on, and under which user name. To open the
dialog box, choose Job Options from the File menu on the Prime menu bar. The Job Options
dialog box lists 10 types of jobs, from Find Family (run from the Find Homologs step) to Run
Refinement (run from the Refine Structure step). Specify the host machine and the user name
for each type of job. The default host is localhost. Make sure your schrodinger.hosts file
contains a list of available machines to run on. See the Installation Guide for information on
the schrodinger.hosts file.
2.5.2 Setting Up and Launching Jobs
Though you specify the machines used to run jobs in the Job Options panel, you select Prime
job settings and launch jobs from the Prime step panels. This can be as simple as clicking an
action button, such as Search. In other steps, you select the type of job from a Task menu and
then launch the job by clicking Run.
Prime 2.1 User Manual