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. --- //
$CRYOSPARC_HOSTS[] = array('CRYOSPARC #1' => 'IP1');
//$CRYOSPARC_HOSTS[] = array('CRYOSPARC #2' => 'IP2');
define('CRYOSPARC_PORT', "39001");

Replace IP1, 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 or 2D classification 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.