https://github.com/diamondlightsource/python-icebreaker
Ice gradient estimation for cryoEM
https://github.com/diamondlightsource/python-icebreaker
Last synced: 3 months ago
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Ice gradient estimation for cryoEM
- Host: GitHub
- URL: https://github.com/diamondlightsource/python-icebreaker
- Owner: DiamondLightSource
- License: bsd-3-clause
- Created: 2021-07-01T13:39:18.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2024-10-11T09:49:30.000Z (7 months ago)
- Last Synced: 2025-02-17T23:17:39.593Z (3 months ago)
- Language: Python
- Homepage:
- Size: 103 KB
- Stars: 9
- Watchers: 5
- Forks: 6
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ICEBREAKER
The Icebreaker software for ice gradient estimation and removal on cryoEM micrographs.
External job for calling IceBreaker grouping within Relion 3.1
in_parts is input star file from relion picking job
in_mics is previous grouping job directory
Run in main Relion project directory
## Running as a RELION External job
Icebreaker provides a number of command line tools that wrap the core functionality in a way that is friendly for the RELION External job. These tools are:
```
ib_job
ib_group
ib_5fig
```
If Icebreaker is installed in your Python environment then these can be used directly as the executables for a RELION External job.
## Processing the micrographs
To process the micrographs use the `ib_job` command line tool
As an input, it takes a .star file with a list of micrographs to process, e.g. micrographs_ctf.star
In the 'Params' tab, you have to add a label **mode** which can take values **group** (it will group areas with similar ice thickness) or **flatten** (it will improve contrasts locally trying to remove the ice gradient).
In the Running tab use the slider to select the number of threads.
The output from this job is a new set of micrographs.
## Processing the particles
This is done using the `ib_group` command line tool. As 'Input micrographs' it takes micrographs 'grouped' with the previous script. As 'Input particles' any star file with particles from jobs like Extract particles, 2D classes, etc. As a result, additional parameter column (\_ibIceGroup) with estimated ice thickness value for each particle will be added.
## Using the job templates
To make it easier to get started running Icebreaker from Relion, you can use one of the template star files *ib\_job\_template\_GROUP\_MODE.star*, *ib\_job\_template\_FLATTEN\_MODE.star* or *ib\_group\_template.star*. To use a template:
1. Copy one of the templates to your Relion project directory as *.gui\_externaljob.py*
2. Select the External job type
3. Click Jobs -> Load job settings
4. Change the placeholder input names to select your input files
5. Choose your running options and run the job as normal
## Runnnig outside of RELION
There are a number of command line tools which can be used outside of the RELION context. These are:
```
ib.micrographs_group
ib.micrographs_flatten
ib.particles_group
ib.five_fig
```
The functionality of these tools correspond, respectively, to `ib_job` in **group** mode, `ib_job` in **flatten** mode, `ib_group` and `ib_5fig`.
The required command line options can be seen by using the `--help` flag.