Job: Gctf (Wrapper) (Legacy)

At a Glance

Estimate the contrast transfer function parameters for exposures using Gctf.

Description

This job is a wrapper around Gctf (Zhang 2016). See the original publication for an explanation of the algorithms employed by Gctf and recommendations for the diagnostic plots.

Note that this job is a Legacy job, and does not show up in the job builder by default.

Inputs

Exposures

Gctf 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.

Particle stacks

Gctf optionally accepts particle stacks for local adjustment of CTF parameters. This process does not use a reference 3D structure. GCTF’s local refinement of CTF parameters is only expected to improve results that are already at relatively high resolution (e.g., better than 4 Å).

Commonly Adjusted Parameters

Abs path to Gctf executable

This dropdown selects from a list of Gctf binary names for various versions of CUDA. Note that these binaries must be installed at deps/external/gctf-1.06/bin/ within the cryosparc_worker directory.

Abs path to CUDA version

Publicly available Gctf binaries only support CUDA ≤ 8, but CryoSPARC uses a newer CUDA version. Users of this wrapper must therefore download and maintain their own copy of the CUDA 8 toolkit. The toolkit can be installed without root access by downloading the CUDA 8 runfile from NVIDIA and installing it in a location of the user’s choice.

As Gctf is compiled code, only the runtime toolkit is required. Carefully inspect the options while using the runfile and avoid installing any features other than the toolkit.

The absolute path of the lib64 directory in this toolkit installation must be provided to this parameter.

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. Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).