Appion

h1. CryoSPARC

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

h2. Installing

Install "MongoDB PHP Driver":https://docs.mongodb.com/ecosystem/drivers/php/. 

For CentOS 7 our centos7AutoInstallation.py does this. 

For CentOS 6, "update to PHP 5.6 on CentOS 6 using remi repository":https://blog.tinned-software.net/update-to-php-5-6-on-centos-6-using-remi-repository/. Then install "MongoDB PHP Driver":https://secure.php.net/manual/en/mongodb.installation.pecl.php. 

Add the following lines to your myamiweb/config.php

<pre>

// --- cryoSPARC host name and port number. --- //

$CRYOSPARC_HOSTS[] = array('CRYOSPARC #1' => 'IP1');

//$CRYOSPARC_HOSTS[] = array('CRYOSPARC #2' => 'IP2');

define('CRYOSPARC_PORT', "39001");

</pre>

Replace IP1, with the name or IP address of your host running cryoSPARC v2.

h2. Usage

In Appion menu click on cryoSPARC link.

!thumbnail_image.png!

Enter Project and Job ID for a cryoSPARC v2 3D refinement or 2D classification job and click Submit.

!thumbnail_image1.png!

This renders a page similar to this one:

!cryosparcs.png!

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:

!thumbnail_image2.png!

Summary link shows cryoSPARC output similar to above.