CryoSPARC » History » Revision 6
Revision 5 (Sargis Dallakyan, 10/22/2019 06:45 PM) → Revision 6/9 (Sargis Dallakyan, 10/22/2019 06:47 PM)
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.
!c2.png!
!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:
!c1.png! !thumbnail_image2.png!
Summary link shows cryoSPARC output similar to above.