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CryoSPARC » History » Version 6

Sargis Dallakyan, 10/22/2019 06:47 PM

1 1 Sargis Dallakyan 
h1. CryoSPARC
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The user is able to display cryoSPARC v2 3D refinement jobs.





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h2. Installing





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





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For CentOS 7 our centos7AutoInstallation.py does this. 





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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. 





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Add the following lines to your myamiweb/config.php





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<pre>





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





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





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





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define('CRYOSPARC_PORT', "39001");





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</pre>





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





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h2. Usage





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In Appion menu click on cryoSPARC link.





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





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!c2.png!





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This renders a page similar to this one:





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!cryosparcs.png!





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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.





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Users can go back and add/remove cryoSPARC jobs as show below:





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!c1.png!





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Summary link shows cryoSPARC output similar to above.