# 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](https://developer.nvidia.com/cuda-80-ga2-download-archive) and installing it in a location of the user’s choice.

{% hint style="info" %}
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.
{% endhint %}

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](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/motion-correction/job-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).