Job: CTFFIND4 (Wrapper)

At a Glance

Estimate the contrast transfer function parameters for exposures using CTFFIND4.

Description

This job is a wrapper around CTFFIND4 (Rohou and Grigorieff 2015). Please read the license terms below.

Documentation and explanation of various parameters and plots are available from the Grigorieff Lab.

CTFFIND4 License Terms

The Janelia Research Campus Software License 1.2 Copyright (c) 2018, Howard Hughes Medical Institute, All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of the Howard Hughes Medical Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Inputs

Exposures

Unlike CryoSPARC’s Patch CTF job, CTFFIND4 can process either movies or micrographs. If movies are provided, they will still need to be motion corrected before further processing can occur in CryoSPARC.

When using movies as input, ensure movie frames are gain corrected before import to CryoSPARC. Movies connected to CTFFIND (Wrapper) which were imported into CryoSPARC with a separate gain correction file will not work, as CryoSPARC does not bake gain correction into the movies during import. When you connect these movies to CTFFIND it will fail to recognize the gain correction and performance will likely suffer as a result.

Commonly Adjusted Parameters

For convenience, the parameter tooltips reproduce help messages from CTFFIND4. For further assistance and suggested values, please consult the CTFFIND4 documentation.

Outputs

Exposures

Exposures with CTF estimates. Exposures will be of the same type (i.e., micrographs or movies) as the inputs.

Common Next Steps

If inputs were movies, Patch Motion Correction is typically the next step. Otherwise, the micrographs are ready for particle picking and extraction.

References

1. Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Journal of Structural Biology 192, 216–221 (2015).