CryoSPARC¶

The user is able to display cryoSPARC v2 3D refinement jobs.

Installing¶

Install MongoDB PHP Driver.

For CentOS 7 our centos7AutoInstallation.py does this.

For CentOS 6, update to PHP 5.6 on CentOS 6 using remi repository. Then install "MongoDB PHP Driver".

Add the following lines to your myamiweb/config.php

// --- cryoSPARC host name and port number. --- //
define('CRYOSPARC', "yourhost");
define('CRYOSPARC_PORT', "39001");

Replace yourhost, with the name or IP address of your host running cryoSPARC v2.

Usage¶

In Appion menu click on cryoSPARC link.

Enter Project and Job ID for a cryoSPARC v2 3D refinement job and click Submit.

This renders a page similar to this one:

In the top left it shows 3D map. Wait for it to load. Depending on your network connection and the size of the map it might take a minute to load the map. Visit http://nglviewer.org/ngl to learn about mouse controls. At the bottom it shows output from cryoSPARC.

Users can go back and add/remove cryoSPARC jobs as show below:

Summary link shows cryoSPARC output similar to above.