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| The program is provided with a graphical interface for easy configuration and data inspection, and builds upon the capabilities of [[auto3dem:home|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 program is provided with a graphical interface for easy configuration and data inspection, and builds upon the capabilities of [[auto3dem:home|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. | ||
| + | ---- | ||
| ===== Installation ===== | ===== Installation ===== | ||
| - | * Download the file [[http://cryoem.ucsd.edu/programs/code/autortm_151124.tar.gz|autortm_151124.tar.gz]] and uncompress it | + | * The installation procedure is valid both for Linux and Mac OSX systems. |
| + | * Download the file [[http://cryoem.ucsd.edu/programs/code/autortm_151124.tar.gz|autortm_151124.tar.gz]] and uncompress it | ||
| tar xvfz autortm_151124.tar.gz | tar xvfz autortm_151124.tar.gz | ||
| Line 26: | Line 27: | ||
| ==== Notes ==== | ==== Notes ==== | ||
| - | The procedure will install a complete python environment, with the all the modules and libraries required by the program, and the external software packages [[http://lsbr.niams.nih.gov/bsoft/|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''. | + | The procedure will install a complete python environment, with the all the modules and libraries required by the program. |
| - | The procedure will also 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 | + | |
| + | The procedure will also install two external software packages, [[http://lsbr.niams.nih.gov/bsoft/|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 | ||
| - set the path to the chimera binary in the //cpath// variable inside the file //src/session.py// in your installation directory | - set the path to the chimera binary in the //cpath// variable inside the file //src/session.py// in your installation directory | ||
| - save a default session configuration file and modify its parameter //chimera_path// | - save a default session configuration file and modify its parameter //chimera_path// | ||
| + | ---- | ||
| ===== Usage ===== | ===== Usage ===== | ||
| - | /*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. | + | The program is launched from a terminal using the command ''**autortm**''. It displays a graphical interface where you can access to a session menu where you set up an acquisition session. |
| + | ==== Sessions ==== | ||
| + | A session contains all the information to process a specific sample. The configuration can be saved in a session file (.ars extension) for future use. Critical parameters are the microscope settings (voltage, spherical aberration and pixel size) and the information on the sample (amplitude contrast and approximate diameter of the particle). Depending on the computing system you are using, you can also modify the number of processors used for different tasks during the analysis. A special option, ''Run multiple models in parallel'', allows to run multiple model computations in parallel, but it only works on systems that use the Torque/PBS queue system to launch multiple jobs. Additional parameters determining a session, such as the version of CTFFIND to use (default: 3, version 4 currently available only on Linux systems) or the path to the Chimera executable, can only be modified in the .ars session file, using a text editor. | ||
| + | /* | ||
| In order to get familiar with the module, here is provided a [[http://cryoem.ucsd.edu/programs/code/TestCaseLFSC.tar.gz|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. | In order to get familiar with the module, here is provided a [[http://cryoem.ucsd.edu/programs/code/TestCaseLFSC.tar.gz|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 ===== | ||
| + | ---- | ||
| + | ===== Support ===== | ||
| + | The program was written mostly as a proof-of-concept for real-time, high-throughput single particle microscopy. Currently it is not actively developed, and only minimal support is provided. If you have questions, please contact the authors. | ||
| + | ---- | ||
| + | ===== License ===== | ||
| + | |||
| + | AutoRTM is free to use for educational, research and non-profit purposes (see [[autortm:license|LICENSE]]). | ||
| + | |||
| + | ---- | ||
| + | ===== Funding ===== | ||
| + | |||
| + | Development of AutoRTM has been funded by NIH Grant R01-GM087708 (2010-2014). | ||
| + | ---- | ||
| ===== Credits ===== | ===== Credits ===== | ||
| The software was developed by Giovanni Cardone and Xiaodong Yan. | The software was developed by Giovanni Cardone and Xiaodong Yan. | ||
| + | ---- | ||
| ===== Citation ===== | ===== Citation ===== | ||
| If you find this software useful for your research project, please cite: | If you find this software useful for your research project, please cite: | ||