CryoSPARC » History » Revision 3
Revision 2 (Sargis Dallakyan, 03/06/2019 07:25 PM) → Revision 3/9 (Sargis Dallakyan, 03/06/2019 07:36 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".
Add the following lines to your myamiweb/config.php
<pre>
// --- cryoSPARC host name and port number. --- //
define('CRYOSPARC', "yourhost");
define('CRYOSPARC_PORT', "39001");
</pre>
Replace yourhost, 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 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.