/python-icebreaker

Ice gradient estimation for cryoEM

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

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.