Orion 2021.1.1

Selected Training Videos

New training and demonstration videos have been introduced, with special attention to UI features that were changed or introduced in this version of Orion. You can find links to them in this section and in relevant places elsewhere in this manual. For a list of all tutorial videos, see Orion Video Tutorials.

Data organization video

The features for organizing data have been revamped significantly. For an introduction, try this video: Data Organization in Orion.

Discussion board videos

Discussion boards are a new user interface feature introduced in this version, accessed via an icon on the Project Data page: Introducing Discussion Boards

We welcome your feedback on discussion boards after you have used them: Using Discussion Boards.

For more about discussion boards, see Discussion Boards.

3D modeling videos

There are new badge and list features on the 3D Modeling page. Here is an introduction: Badges and Lists in Orion.

There are several more new videos about 3D modeling at Orion Video Tutorials.

Highlights

  • This release introduces a revamped Project Data page which now uses a path- and folder-based file system for data organization.

  • A desired data location can be specified when uploading data, creating subfolders, or launching a Floe on the Job Form.

  • Users will be prompted to triage shared data and collections as part of data migration.

  • A “What’s New” dialog is now displayed on the Home page when users first login to Orion.

  • Many enhancements have been made to 3D Modeling page, including several new tools for protein editing.

  • Molecules, proteins, and other components of a dataset can now be identified using badges.

  • Tooltips in the 3D Viewer have been enhanced.

  • Support for grouping promoted parameters has been added to the Job Form.

  • A new discussion boardBeta feature is now available.

  • This release introduces Orion stack protection through rate-limiting.

  • Job cost email alerts can now be created.

  • A dedicated Organization Data project has been added. The data in this project are available to all Organization users and are prepopulated with OpenEye Data such as Collections used for virtual screening.

  • New Floes have been added to Floe packages including:

    • Non-Equilibrium Switching (NES) Floes in the MD Floe package.

    • Cluster Poses, FastROCS, and FreeForm Pose Floes in the Large-Scale-Floes package.

    • Large-Scale Reaction Enumeration Floes in the Generative Design Floe package.

  • Dataset writing is now more robust with field names of different types.

General

New Features

  • Orion stack protection through rate-limiting has been implemented.

  • Job cost email alerts are now available. Organization admins can set Job cost limits alerts for the entire organization on the Profile page. In addition, users can set Job cost limits alerts and Job termination thresholds for their own jobs on the Profile page. Job cost alerts can also be set prior to running a job on the Job Form. These cost thresholds can be updated while a Job is running on the Job Status page.

  • This release introduces a new Discussion BoardBeta. Saved discussions may contain notes, images, or snapshot links of the 3D Modeling or Analyze pages. Discussions are accessible to all team members.

  • Substructure searching is now accessible from the databar filters. This functionality was previously available only on the Analyze page.

  • Cubes which are being throttled now show up with special coloring.

  • More information has been added to Job Debugging Data.

  • A new instance-draining state has been added, which allows jobs to continue running but prevents new jobs from using the instance.

  • Dataset writing is now more robust with field names of different types. For new data being written to a dataset, it will be cast/coerced/promoted to the type of the existing dataset field. This matches what drconvert does. When writing records, if an incompatible type of data for a given field name is seen, the writer generates a new alternate field and stores the data in an alternate field rather than failing the writing process.

Home

New Features

  • A “What’s New” dialog is now displayed on the Home page when users first login to Orion.

Project Summary

New Features

  • A dedicated Organization Data project has been added. Data in this project is visible to all Organization users and can be accessed from any project. In addition, the Organization Data project is pre-populated with OpenEye-supplied data such as the Brood database, OpenEye-prepared third-party vendor collections for virtual screening, tutorial datasets, and other data that can be used as input to some of the included Orion Floes. Note: The Organization Data project is only visible to Organization admins in the list of projects in the Navbar and Home page.

Minor Bug Fixes

  • Organization admins now have control over the listing of projects on the Home page and Navbar on the Project Summary page. Organization admins can now toggle between ‘Show All’ Organization projects and ‘Show Own’ projects.

Project Data

New Features

  • The Project Data page has been overhauled and now uses a folder-based file system for organizing your data, instead of a flat view.

  • Within a project, data are organized into three main areas:

    • My Data – your private data. No other users have access to this data.

    • Team Data – data that are available to all project members.

    • Shared Spaces – data that are available to select project members, i.e. shared data among the selected project members.

  • New folders can be created from the Project Data page, when uploading data, and when launching a Floe from the Job Form.

  • A dedicated Organization Data project is available to everyone in the Organization and is located above the Project Data folder hierarchy. Data in this project is visible to all Organization users and can be accessed from any project.

  • The path to a desired data location can be specified when uploading data, creating subfolders or when launching a Floe on the Job Form.

  • Folders and subfolders can be added to the Favorite Folders space for quick and easy access.

  • Data are now shared by creating a workspace in the “Shared Folders” main folder. Permissions can be set for each user added to the workspace.

  • Drag and drop functionality allows users to move collections, datasets, and/or files to the three main data areas, Trash can or other subfolders.

  • String Search will search within the current folder or all project folders, i.e., My Data, Team Data or Shared Spaces.

  • Discussion boardsBeta can be created within a workspace to highlight and annotate data within that workspace, and can be viewed by all of that workspace’s members.

  • As part of the data migration, users will be prompted to triage shared data and collections. Collections now belong to projects.

3D Modeling

New Features

  • The 3D Viewer list is now record-focused.

  • Badges to identify molecules, proteins and other components of datasets have been added to the 3D Viewer list.

  • Tools for protein editing, including protonation state modification, capping terminal residues, and residue mutation have been added.

  • When mutating protein residues, multiple residues can be selected and users can walk through applying a mutation to each residue in the selected set.

  • Most of the small molecule editing tools can now be applied to proteins as well.

  • The 3D molecule editor now contains the same set of molecular fragment templates as the 2D sketcher.

  • An edited protein can be saved as a new dataset.

  • A new receptor in OEDesignUnit (DU) display has been added.

  • OEDesignUnit components can be edited and saved in place.

  • Receptor ligands can be edited but not in place. Users need to make a copy of the ligand before editing. Note: Receptor proteins cannot be edited.

  • More options to save edited small molecules are now available.

  • Users can edit datasets they don’t own in place but need to save them to new datasets.

  • A Discusson boardBeta was added for collaboration and replaces Saved Views. Saved Discusson boards can be retrieved from the Discussion menu on the Project Data page.

Minor Bug Fixes

  • Improvements have been made to the small molecule editing tools.

  • Depiction tooltips in the list appear more reliably.

Analyze

New Features

  • Improvements have been made to Data Handling. Users can now set the visibility for each column for each component of the user interface from the Data Handling dialog.

  • A Discusson boardBeta was added for collaboration and replaces Saved Views. Saved Discusson boards can be retrieved from the Discussion menu on the Project Data page.

Major Bug Fixes

  • Spreadsheet fields now render correctly when users scroll to the right side of the spreadsheet.

  • Layout issues when using multiple plots in trellis mode have been fixed.

  • Molecules can now be sent to a Floe that takes a molecule fragment as input, for example, the Brood Floe.

Minor Bug Fixes

  • Selecting conformer points in the Scatter plot no longer fails intermittently.

  • Saved color settings now persist.

Floe User Interface

New Features

  • Jobs Page:

    • Support for grouping promoted parameters has been added to the Job Form.

    • Support for a Job output folder path has been added to the Job Form. The default folder for Job output is ‘My Data’, however, users can select a different folder or create a new one.

    • Job Cost alert and termination thresholds can now be set on the Job Form. The default values are inherited from the ‘My Job Cost Limits’ set on the users’ Profile page. Job Cost thresholds for any given job can be disabled by clearing the current value or setting the value to zero. The values of these thresholds can be adjusted on the Job Status page after a job has been launched.

    • Cubes in a running job are now colored specially when they are being throttled. More details are available in the Floe help.

Major Bug Fixes

  • Jobs Page:

    • A bug has been fixed that caused Job parameters for jobs launched from the Orion command line interface (OCLI) from being displayed on the Job Status page.

    • A bug that prevented the Job Form from opening for certain Floes has been fixed.

Minor Bug Fixes

  • Jobs Page:

    • An issue that sometimes caused duplicate input or output parameters to appear in the Job Form has been fixed.

Data Sources

New Features

  • Minor internal improvements have been made to FastROCS, MaaS, and MMDS.

Admin Mode

New Features

  • Options to customize Job Cost email alerts for Organization admins have been added.