I finally figured this out, and wanted to clarify on here for anyone encountering this problem in the future.
here’s how to import particle coordinates only, then map them to your micrographs within cryosparc.
- either import your micrographs or do your alignments within cryosparc.
- import particle stack (leave the mrc field blank) and click “ignore raw data”. At the top, drag and drop from cryosparc the micrographs that you will be linking those particles to.
- Open up your particles.star file on your computer and look at the micrograph filenames for each particle. Take note here the suffix of each.
- Do the same as above except now with your micrographs: either the ones that have been aligned in cryosparc or the ones that you have aligned and imported elsewhere.
- Figure out how many characters need to be removed from the end of each in order for them to match perfectly. This includes the file extension and any punctuation each counting as one character.
- The above two integers need to be inputted when you are importing your particle positions under the fields " mic path suffix to cut" (for the aligned images) and “particle path suffix to cut” (for the paths within your particles.star file).
- for example your particles contains entries such as “…micrograph01_A.mrc” and the cryosparc aligned images outputs files such as “…micrograph01_rigid_aligned.mrc” then the integers to put in the above fields are 6 for “particles path suffix to cut” and 18 for “mic path suffix to cut”.
hope this helps someone!