Job: CTFFIND4 (Wrapper)

How to use the wrapper for CTFFIND4 available in CryoSPARC.

Description

Estimate CTF parameters of micrographs using CTFFIND4 4.1.10. CryoSPARC v2 provides a wrapper to CTFFIND4: Alexis Rohou and Nikolaus Grigorieff. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Journal of Structural Biology, 192(2):216–221, November 2015. Please see the CTFFIND4 License Terms below.

Input

• Aligned/motion-corrected micrographs

• Gain-corrected Movies

Common Parameters

• Only process this many micrographs: Set a value if you wish to estimate CTF for only a subset of all micrographs, e.g., if you want to build a template for automatic particle picking.

Output

• Micrographs/Movies with CTF information

Notes

When using Movies as input, ensure movie frames are gain corrected (CryoSPARC will allow you to import a movie with no gain correction file). Movies connected to CTFFIND which were imported into CryoSPARC with a gain correction file will not work, as gain correction is not baked into the movies after being imported- they are calculated on the fly. Therefore, when you connect these movies to CTFFIND, it will fail to recognize the gain correction.

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:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. 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.
3. 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.

Common Next Steps

• Particle picking