1. Project directory management

As Relion tutorial said: 

1. It was suggested to create a single directory for a structure after relion-3.1.

2. Put your data in the project directory. As the relion tutorial said: for some reason, you do not want to place your movies inside the relion project directory, then inside the project directory, you can also make a symbolic link to the directory where your movies are stored.

3. When import different data set, set different optics groups for each of them. 




2. MotionCor2 related problem

Since MotionCor2 requires an academic license to download directly, we cannot download it. Please download the package from https://emcore.ucsf.edu/ucsf-software by submitting a Google Form before calculation and inform us, then we could install it for you. 




3. Relion_lock error

If you encounter the following error while using relion:


WARNING: trying to read pipeline.star, but directory .relion_lock exists (which protects against simultaneous writing by multiple instances of the GUI)

Please check the following：

  • 1. Check the permission of the project directory. For files in the current directory, the login account should have read and write permissions. Use ll -a to check it. If not, add permissions.

  • 2. Check the disk's occupation. Is the system partition full(df -h)? If it's full, delete unneeded experimental data.

  • 3. Check .relion_lock folder. If it exists, delete the .relion_lock file in the current directory.




4. Generate an empty PDF

If you encounter an error below: 


Did not find any of the expected EPS files to generate a PDF file
 + Will make an empty PDF-file in CtfFind/job005/logfile.pdf


and cannot open logfile.pdf, usually, there are three possibilities: 

  • 1. You can open other results (like Thor Ring or Motion result) besides PDF, and you can use results for later calculation. In this case, the error will come together with a gs error. Continue calculation and contact us to solve it.

  • 2. You cannot open any other results (like Motion micrographs or CTF Thor Ring), which means the calculation failed. To solve this error, first check the import job, see if there are any movies or micrographs imported successfully. If movies or micrographs import successfully, send the project directory to us, and we will check the software logs then fix it.

  • 3. If this error only appears in the PostProcess job, please check if the MaskCreate job's "Initial threshold" parameter is too large. To modify the parameter, using UCSF chimera to open Refine 3D result mrc (run_class001.mrc). Move the "contour level" up and down to find a suitable level, which shows absolutely no noisy spots outside the protein area. The initial threshold is the same as the suitable contour level. For more information, please refer to relion tutorial Mask Creation Part: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion31_tutorial.pdf