Download Cryosparc
Nevada Biernat
Another thing I notice is there is no config.sh inside the worker directory. The installation did seem to potentially end prematurely when it had trouble creating my cryosparc user account (that seems to happen while trying to reinstall inside this cryosparc directory, but replacing the database content with my old database makes the cryosparc user account available to log in with again).
Hi @afrangaj, this indicates that you need to reconnect your worker so that the master module registers the new path in the database, you can do this from the cryosparc_worker directory with the bin/cryosparcw connect command.
I encountered the exact same issues as @afrangaj above (and had a similar situation). I was updating from version 2.15 to 3, and the installation was unsuccessful through cryosparcm update, so I ended up doing a fresh reinstall of cryoSPARC v3.0 after backing up my database.
Go into the cryosparc_worker directory and run ./install.sh --license --cudapath , where and are your license and path to cuda (e.g. /usr/local/cuda). This step will generate the missing config.sh file.
It may be helpful to provide a little more info about your workflow. Did you start off in cryosparc and then go to bayesian polishing? If so, did you verify that your particle coordinates matched up between relion and cryosparc? Looking at these I would guess you have an issue in coordinate conversion, and so your polishing was performed at non-particle locations on the micrograph.
I believe the problem is you need to use the --swapxy flag in csparc2star.py for particles extracted in cryosparc. I often do a quick test of the coordinates by extracting a small subset of particles (1k) in relion based on the homo-ref star file from csparc2star, then take these to 2D class.
More on this here, just ignore my comments on flipping an axis as I was mistaken.
Thanks for reporting this bug, which we are planning to fix in a future release.
Once the fix has been released and applied, it will take an additional
cryosparcw update for the fix to become effective . Should
cryosparcw update --override become necessary before the fix is released, applied and effective, please manually remove the directory
After running
cryosparcm update and, if needed,
cryosparcw update
you may test the validity of the the GPU configuration either through the command line or the GUI.
As of CryoSPARC v4.4, the test includes a check of the nvidia driver version.
Welcome to the forum @svalen.
Please can you paste your terminal output as text.
Before deleting the sock file, one should always confirm that no processes related to the given CryoSPARC instance are running, keeping in mind that a computer can run multiple CryoSPARC instances (if certain requirements are met). For this purpose: under the Linux account that runs CryoSPARC processes, run
cryosparcm stop
ps xww grep -e cryosparc -e mongo
and kill (not kill -9) processes related to the given CryoSPARC instance, but not processes related to other CryoSPARC instances that may also be running on the computer.
For confirmation that no more relevant processes are running, again:
ps xww grep -e cryosparc -e mongo
Only then should sock files belonging to the given CryoSPARC instance be removed.
Does this help?
Sorry, but I accidentally removed the sock file while the cryosparc is running. Then the cryosparc can not restart as this issue Error starting cryosparc: "Could not get database status" - #9 by wtempel say. How can I solve this problem. I am really regreting for not stopping cryosparc first. Thank you very much!!
the multistep procedure (simple CryoSPARC stop, discovery and confirmed termination of stale processes and then, and only then, deletion of stale socket files, details) of a complete CryoSPARC shutdown.
After the complete CryoSPARC shutdown, please attempt
cryosparcm start.
If you encounter any problems, please post
I have 4000 frames now, but some have very thick ice and huge cracks, so I want to go through each frame one by one in cryosparc and make a selection. How can I achieve this functionality? In relion I usually do it in the manual picker program.
I upgraded to cryosparc v4.0.0. I can access my project files and download the files form my updated cryosparc instance, but when I try to build a new job I get an error saying that the lock file for my project is not found.
I know that the new version uses lock files to track which instances created a project but I do not know what to do if there is already a project in attached to the cryosparc instance but without a lock file. I also tried to detach the project from the cryosparc instance but got the same error saying the lock file was missing.
My workaround, briefly, I changed the path to my project files, and attached the project with the new path to my cryosparc instance as a new project. This generated a lock file in my project directory. I then changed the path to my project files back to the original. Now that there is a lock file in the project directory so I can queue jobs in the original P3 project in my cryosparc instance. However, there is a ghost P4 project directory in my cryosparc instance, but I think I can just ignore that.
Oh definitely. I started liking cryosparc a lot, but it is still missing some basic functionalities as you mentioned in another thread. Addition to your suggestions, I think there should be a tool to manually dragging or manipulating 2D classes to recenter particles belong to that class. I guess you suggested some re-centering based on center of mass. That would be good too. Subset selection, resuming a failed job are some other missing functions.
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