CryoSPARC » History » Revision 5
Revision 4 (Sargis Dallakyan, 03/06/2019 07:39 PM) → Revision 5/9 (Sargis Dallakyan, 10/22/2019 06:45 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. --- // $CRYOSPARC_HOSTS[] = array('CRYOSPARC #1' => 'IP1'); define('CRYOSPARC', "yourhost"); //$CRYOSPARC_HOSTS[] = array('CRYOSPARC #2' => 'IP2'); define('CRYOSPARC_PORT', "39001"); </pre> Replace IP1, 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 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.