Localized Reconstruction Notes
Here are some CSSB specific notes on how to run localrec with Relion 3.x. The Scipion 2.0 GUI version has not been tested, but localrec 1.2.1 needs Relion 1.4 but Scipion 2 comes with Relion 3.
Note: Since September 2019 the Scipion Relion plugin can also install older Relion versions, but this has not been tested for localrec yet.
Normally the task is done in 4 steps which can be combined:
- Prepare particles
- Create subparticles
- Extract subparticles
- Reconstruct subparticles
In the latest localrec version step 4 cannot be done, since the Relion 3.x star file contains entries not recognized by Relion 1.4 (e.g rlnCtfMaxResolution).
CSSB-specific Quick Start Guide
Create a marker file
Use UCSF Chimera to create your marker file. In the example below it is called marker.cmm.
Create your cluster submission script
Use this template for the DESY maxwell cluster, adapt the command line parameters to your settings and save it as e.g. localrec.sh:
Submit your cluster script
Import the extracted information in Relion3
The output directory (from the example above) is called SubParticles.
The Relion import patterns are therefore:
- SubParticles/*_subparticles.star for the coordinates
- SubParticles/*_subparticles.mrcs for the particles
Now do the reconstruction in Relion 3.