ScipionCloud AMI manual

Laura edited this page Jun 18, 2018 · 4 revisions

ScipionCloud AMI manual

Remote desktop (noVNC)

To resize screen clicks on the Settings icon and choose Remote resizing as Scaling mode:

noVNC - resize

To disconnect from the session click on the little arrow that appears on the left (see menu below) and click on the last option:

noVNC - disconnect

IMPORTANT!! Do not disconnect from the top right corner, as in a physical machine. If you do so the machine will need to be reboot

Software installed

The AMI is based on Ubuntu 16.04 server AMI.

The following software is installed on the machine:


The latest stable release of Scipion (from github) is installed at: /usr/local/scipion

There is an icon on desktop that starts scipion. There is also an alias to run it from terminal.

Note: Both alias and desktop shortcut start Scipion through VirtualGL, this is to make chimera work on GPU powered machines.

EM packages

  • Ctffind4 4.1.8
  • Gctf 1.06
  • Gautomatch 0.53
  • Eman 2.12
  • Frealing 9.07
  • Motioncor2 1.0.2
  • Motioncorr 2.1
  • Relion 2.0
  • resmap 1.1.5s2
  • Spider 21.13
  • chimera 1.10.1

To verify installed packages type:

scipion install --help

And to install latest version of a package:

scipion install package-name

Relion is compiled with CUDA support.


  • Nvidia driver version 387
  • CUDA 7.5, 8.0 and 9.1 (default cuda links to 7.5) on /usr/local/.
  • TurboVNC 2.1.1 on /opt/TurboVNC.
  • VirtualGL 2.5.2 on /opt/VirtualGL.
  • noVNC on /opt/noVNC.
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