Issues

CryoSPARC project needs to be moved

The easiest way to continue working with a CryoSPARC project after moving it to a different directory is to:

1. Detach the project from CryoSPARC.
2. Move the project directory to its new location.
3. Reattach the project in CryoSPARC.

Recommended procedure

Always detach the project from CryoSPARC before moving its directory. This ensures that the project is properly removed from the CryoSPARC database before it is moved.

1. Detach the project

In CryoSPARC, open the project and select Detach Project.

2. Move the project directory

Move the project folder to its new location. For example:

Bash

mv /data/project/bio/<project-name>/CS-project /data/project/cls/<project-name>/CS-project

3. Reattach the project

In CryoSPARC, use Attach Project to add the project from its new location.

CryoSPARC project was moved

If you moved the project directory before detaching it from CryoSPARC, the project may still be registered in the CryoSPARC database under its old location.

In this case, you can mark the project as deleted in the database and then attach it again from its new location.

Use with caution

The following procedure directly modifies the CryoSPARC database. Make sure that you specify the correct project ID and that the project directory has already been moved to its new location.

On a Merlin 7 login node, start the CryoSPARC interactive Python session:

Bash

/data/user/$USER/cryosparc/cryosparc_master/bin/cryosparcm icli

CryoSPARC path

If your CryoSPARC installation is in a different directory, correct the path to cryosparc_master in the command above. For example, /data/user/$USER/cryosparc_beta/cryosparc_master/bin/cryosparcm icli

Once inside the interactive Python shell, specify the project ID you want to remove from the database. For example, for project P10:

Python

db.projects.update_one({'uid': 'P10'}, {'$set': {'deleted': True}})

Note

Replace P10 with the ID of the project you want to remove from the database.

After running the command, refresh your CryoSPARC browser session.

Next, navigate to the new project directory and remove the cs.lock file:

Bash

cd /path/to/CryoSPARC/project
rm cs.lock

You can then use Attach Project in CryoSPARC to attach the project from its new location.

Check the project path

Before attaching the project, verify that you are selecting the correct project directory and that the project files are intact.

Correct symlinks

When raw data is imported into a CryoSPARC project, the data itself is not copied into the project directory. Instead, CryoSPARC creates symbolic links (symlinks) in the import job directory that point to the original data files.

If you move the data after importing it with an Import Particles, Import Micrographs, or Import Movies job, the original paths stored in these symlinks may no longer exist. As a result, the symlinks become broken and CryoSPARC can no longer access the imported data.

To repair these symlinks, use the replace_cryosparc_symlinks.py script provided on Merlin 7.

Start the CryoSPARC interactive Python session

Start a CryoSPARC interactive Python session by running:

Bash

/data/user/$USER/cryosparc/cryosparc_master/bin/cryosparcm icli

CryoSPARC path

If your CryoSPARC installation is in a different directory, correct the path to cryosparc_master in the command above. For example, /data/user/$USER/cryosparc_beta/cryosparc_master/bin/cryosparcm icli

Once inside the interactive Python shell, indicated by the >>> prompt, execute the symlink-replacement script:

Python

exec(open("/data/project/cls/shared/software/cryosparc/merlin-cryosparc-installation/scripts/replace_cryosparc_symlinks.py").read())

Follow the instructions displayed by the script to identify the affected project and jobs and to replace the outdated paths.

Example

Suppose you want to update all symlinks in every job within the project with ID P6.

Next, select all jobs that should be updated:

Specify the path that should be replaced. In this example, replace:

/data/project/bio with /data/project/cls

Review the proposed changes and confirm them to apply the replacements:

After the operation completes, the script displays a confirmation that the changes were applied successfully and that no errors occurred.

Check the replacement paths carefully

Make sure that the old and new paths are correct before confirming the changes. The script modifies the symlinks for the selected jobs, so an incorrect path replacement may cause the symlinks to point to the wrong files.