When choosing templates for homology modeling (antibody or anything else) it is helpful to highlight how the possible templates differ with respect to cis-trans omega angles. This script highlights all omega angles with an absolute value below a stated threshold for all molecules in the window. Also, groups and group assemblies are created to allow easy re-display.
There are two forms of this new feature, a Discovery Script .pl file, and a pipeline pilot protocol.
For either note that this is intended to be run from DS with an active molecule window containing aminoacids!
The perl script can be installed in to Discovery Studio then accessed from the "Script" pulldown. See Edit/Preferences/General/Script Commands.
The protocol can be added to your DS server and then also to your "My Tools" Tools Explorer. If you don't know how to do this contact support@accelrys.com for help
Briefly:
First open the Protocols Explorer: View/Explorers in the list of Explorers shown make sure that "Protocols" is checked. When it is a Protocol tab will appear.
In the Protocol tab there wil be at least two main sections, The first is called "Discovery Studio", the second will be "
Anything that is in your personal Protocol folder can the be added to your "My Tools" set of Tools and run interactively. To do this first click on "My Tools" in the Discovery Studio sets of Tools (same place as Macromolecules, Simulations, etc.). When you do this My Tools will be visible in the Tools Explorer. Right click in the Tools Explorer to either Insert a new ToolPanel (if you don't have any yet) or select on an existing Panel or Edit and existing one. In the Tool Panel Editor in the "Commands" section (on right) navigate to the functionality that you want to add then click and drag it over to "Development" section (left).
