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AutoRTM is a software package to determine a 3D reconstruction from a single migrograph of icosahedral particles. The approach is fully automated and it is intended to be used during a microscopy session, to gain structural information from a sample while being initially evaluated.

The program is provided with a graphical interface for easy configuration and data inspection, and builds upon the capabilities of Auto3DEM to perform the computations. Once started and configured, the program monitors a target directory, and process each micrograph found as soon as available. Steps performed are CTF determination, particle localization and 3D reconstruction (using the Random Model Computation method). All this information is displayed in the graphical interface. For further information please refer to the article cited below.


  • The installation procedure is valid both for Linux and Mac OSX systems.
  • Download the file autortm_151124.tar.gz and uncompress it
tar xvfz autortm_151124.tar.gz
  • Go inside the directory created and launch the installation, specifying the final directory where to install the program. The directory can not exist at the launch of the procedure
cd autortm_build
./autortm_install <install dir>
  • At the end of the procedure, follow the instructions on terminal on how to set the shell environment
  • Delete the build directory
cd ../
rm -rf autortm_build


The procedure will install a complete python environment, with the all the modules and libraries required by the program.

The procedure will also install two external software packages, Bsoft (ver. 1.9.0) and Auto3DEM (ver. 4.5.2). If, for some reason, the installation is not able to configure the environment to access them from the program, as an alternative you can install the two software separately, and then launch the installation with the options –skip-bsoft and –skip-auto3dem.

Finally the procedure will try to detect a chimera installation, which will be used to visualize 3D models. In case it is not able to find it but you have it, you have two options

  1. set the path to the chimera binary in the cpath variable inside the file src/ in your installation directory
  2. save a default session configuration file and modify its parameter chimera_path


/*Once opened, the LocalFSC module, a help button provides all the basic information on how to use it and on all the different options available in the interface.

In order to get familiar with the module, here is provided a Test Dataset to download, which contains a simulated reconstruction of a ribosome (see article below for details). Specifically, the archive file contains three maps (two half maps and one map from all the particles) and a Chimera marker file with two markers pointing to two domains with different occupancy level.

  • Uncompress the data.
  • Open the tree maps and the marker file in Chimera.
  • Verify that all three maps are overlapping and their pixel size is properly set in the Features→Coordinates menu of the Volume Viewer dialog window.
  • Hide the two half maps.
  • Open the module (Tools→Volume Data→LocalFSC in the main window or Tools→LocalFSC in Volume Viewer).
  • In Settings, point the first and second map to the two half maps.
  • Still in Settings, set the maximum resolution available (i.e. unfiltered out) in the half maps (in this case 10).
  • In the main window, select one of the markers with Ctrl-left click and the press the Estimate button in Resolution. The estimate will be listed in the GUI, and the FSC plot will be shown in a separate window.
  • You can select multiple markers where to estimate the resolution. In this case the program will not show their corresponding FSC plots.


Test Data


The software was developed by Giovanni Cardone and Xiaodong Yan.


If you find this software useful for your research project, please cite:

Cardone G., X. Yan, R. S. Sinkovits, J. Tang, and T. S. Baker (2013) Three-dimensional reconstruction of icosahedral particles from single micrographs in real time at the microscope. J. Struct. Biol. 183:329-341. (