I did not know the easiest method about importing coordinates into cryosparc. My target was to import the coordinates and remove duplicates from particles autopicked in cryosparc. If I only import the particle stack (/My/Path/*.mrcs in job Import Particle Stack), maybe the removing duplicates step would be very difficult. Can anyone tell me the detailed operations?
- Can I import the particles.star file with the parameter rlnCoordinateX/Y?
- Can I import the _autopick.star files directly? (maybe .box files are OK)
- Can I re-write a new particles.cs and .csg to import result group? But I cannot do this in a short time.
I remembered in csparc2star.py, we should add the parameter ‘–swapxy’. I didn’t know whether we should do the similar thing when we import relion files into cryosparc.
ps: My micrograph number was large. The autopicking have not been done now. I hoped to learn about this ahead of time.
First, import the micrographs and run Patch CTF. Then, import the particles .star with rlnCoordinateX/Y but make sure to give the Patch CTF output as the input at the top of the job builder pane. The coordinates will be imported and converted properly - you will see them included in the list of fields from the .star file in the job event log.
--swapxy is deprecated, using it will just print a reminder that it doesn’t do anything anymore. The _autopick.star or .box files can be converted to a single .star file easily, but only a single particles .star input is accepted by cryoSPARC.
Thank you very much! But I still have some questions.
I am new in cryosparc. And I don’t know how to import ithe particles .star with rlnCoordinateX/Y.
Now What I had tried is to use ‘Import Particle Stack’ and input the ‘particles.star’ (generated by relion extract job) and the corresponding particles (.mrcs file type). And then, I hoped to remove duplicate particles between particles picked in cryosparc template picker and the imported particles. There was an error information about lack of particles.location.
I have read your reply carefully. But I still got stuck in how to give the Patch CTF output as the input at the top of job builder pane. I didn’t know which job you mean. Now, I had checked the particles.star file and confirmed the _rlnCoordinatesX/Y information are exactly in the star file. And it might not be recognized in the cryosparc.
Can you tell me more details?
Hey @Yuqi, in the job builder for the Import Particle Stack job, you should connect the
Micrographs full-frame aligned output from the Patch CTF job into the
Source Micrographs input slot:
Then the particles output of the import job should contain the particle locations from the .star file.