Recent Updates to cryoSPARC

October 12, 2018

Here's an overview of the changes to cryoSPARC in versions 2.3 and 2.4:

Low Level Results and Job Builder Updates

New
Added support for low-level results allowing for building advanced jobs
New

New outputs tab when viewing the details of a job

  • Outputs tab displays all job output groups and individual results
  • Easily copy the path of a particular result, download result
  • Detailed tutorial covering the cryoSPARC .cs file format
  • Tutorial Building Jobs in cryoSPARC
New
Job builder will not allow you to queue a job if you do not satisfy the input requirements
Update
Job builder inputs section redesigned to be more user friendly, shows requirements

Methods Updates

New
Wrapper for GCTF Beta (More details)
New
Wrapper for CTFFIND 4.1.10 (More details)
New
Added lowpass filter option under Volume Tools
New

Simulate Data Beta job to create particle images from up to two input volumes at random relative and global alignments

  • The Simulate Data job allows you to create simulated particle images from up to two volumes. The particle images are created by randomly projecting the input volume, applying the specified CTF parameters and adding random white noise to the resulting images. When two volumes are connected, the user can specify a range (in degrees) of random rotations between the two volumes. The relative pose of the two subvolumes will be different in each particle image to simulate a dynamic molecule.
Update

Redesigned Select 2D interactive job (More details)

  • Adds support for quick selection (all/none/invert) and sorting classes by number of particles, resolution, and effective classes assigned
Update
Volume tools can now be used to invert a mask
Update
Added a volume premultiplier to Particle Subtraction to improve scaling of subtracted projections
Update
Added option to not use halfmaps in Particle Subtraction
Update
Plotting projections of generated volume in Ab-Initio Reconstruction instead of slices. Refinements still plot slices

Various Updates

New
Backup & Restore cryoSPARC database through the command line (More details)
Update
New dependency manager for packages and external binaries, making updates and fresh installations more robust
Update
cryoSPARC username now available in cluster submission scripts (More details)
Fixed
After queuing a job in the tree view, you will remain in the tree view when the details view is opened
Fixed
Exposure curation bug fixes (handling NaNs in inputs, can input multiple numerals to edit selections, corrected phase_shift and fit_to values in CTF fit image)
Fixed
Import volumes saves volume to the correct directory
Fixed
Volume tools conversion between map/mask volume types
Fixed
Non-uniform refinement now outputs a mask. Also removed duplicate volume outputs
Fixed
Use per-particle scale factors in particle subtraction
Fixed
CTF error: 'binary not found'
Fixed
CTFFIND same filename issues


Stay Informed

We are always working on new features and updates to v2! Subscribe to the cryoSPARC newsletter to stay on top of new features, updates and best practices for data processing, or follow us on Twitter.

This website uses cookies to ensure you get the best experience. To learn more, please refer to our Privacy Policy