Cryosparc only allows Non-root account(Normal account) to install, use etc. By default use of spuser account installation, the following operations are all based on account spuser (please do not use other account operations);


Tips：

If you install crysoparc yourself, you must install it with a non-root account. We recommend that cryosparc_cache directory is stored under /ssd, cryosparc_database directory is stored under /data, and owner and group must be normal accounts.  Once installed, open the 39000 port in the firewall.


cryosparc common commands：

start:        cryosparcm  start

status:     cryosparcm  status

stop:       cryosparcm  stop

restart:    cryosparcm  restart


How to access:

Enter http://IP:39000 in the browser to access the cryosparc interface, then enter your account number and password.

 

cryosparc update:

If you need to upgrade cryosparc, you need to stop it first(cryosparcm  stop) and then execute the command: cryosparcm update. Once the upgrade is complete, start cryosparc (cryosparcm  start).


creates a new user account  

V2

cryosparcm createuser --email <email_address> --password <password> --name "<full name>"

V3 and V4

cryosparcm createuser --email <email_address> --password <password> --firstname "<given name>" --lastname <family name> --username <full name>



Check cryosparc account information

Open the mongodb of cryosparc:

cryosparcm mongo

Find all users(enter command):

db.users.find({}, { _id: 0, 'emails.address': 1 })

Tips: command "exit" Command can exit MongoDB



 Reset the password

cryosparcm resetpassword --email <email address> --password <newpassword>


Operation before shutting down a workstation:

If you need to shut down the workstation, you need to stop cryosparc (cryosparcm stop) before you shut down the workstation.



How to use topaz


Please fill in the path of topaz

/spshared/apps/miniconda3/envs/topaz/bin/topaz



How to use deepemhancer


Please fill in the path and module path of deepemhancer

/spshared/apps/miniconda3/envs/deepEMhancer_env/bin/deepemhancer

/home/spuser/.local/share/deepEMhancerModels/production_checkpoints


Motiocnor2


motioncor2 it is commercial software and is free for educational users, need to apply and download the installation package. Please note that cryosparc currently only supports version 1.4.5 of motioncor2, and higher versions are not supported yet.