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autortm:home [2015/11/24 16:48]
gcardone
autortm:home [2019/06/19 16:22] (current)
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 ====== AutoRTM ====== ====== AutoRTM ======
-<fc #​800000>​Documentation in progress</​fc>​ 
  
 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. 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.
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   * The installation procedure is valid both for Linux and Mac OSX systems.   * 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+  * Download the file [[http://bakerlab.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
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 The procedure will install a complete python environment,​ with the all the modules and libraries required by the program. 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, [[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 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 ​procedure ​is not able to install these packages or to configure the environment to access them from the program, as an alternative you can install the two software ​manually (they are available in the //a3dm// and //bsoft// subdirectories), and then launch the installation with the options ''​--skip-bsoft''​ and ''​--skip-auto3dem''​. 
 +<WRAP center round important 85%> 
 +The installation of Bsoft and Auto3DEM will fail if some of the libraries that they need are missing. Please refer to their installation instructions to determine their dependencies. 
 +</​WRAP>​
  
-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+Finally the program relies on [[https://​www.cgl.ucsf.edu/​chimera/​|Chimera]] ​to visualize 3D models. Therefore the installation procedure will try to determine the path to the Chimera executalbe. 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//​
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 ---- ----
 ===== Usage ===== ===== Usage =====
-/*Once opened, ​the LocalFSC module, ​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 from where to launch a processing session and monitor ​the progress of the processing. From the interface you can access to session menu where you can set up an acquisition before starting the processing. 
 + 
 +==== Setting up a session ==== 
 +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. 
 +==== Launching a session ==== 
 +Once a session is properly set up, from the main interface ​it is possible to specify the ''​Directory to monitor'',​ that is the directory where the acquisition system controlling the microscope will store the images acquired, and the ''​Directory for processing'',​ where all the results from the analysis will be stored. At this point you can press the button ''​Start monitoring'',​ and the program will start to process each micrograph acquired as soon as it is stored in the given input directory. At any point you can stop the processing of further images by pressing the same button (now ''​Stop monitoring''​):​ if at that moment a micrograph is being processed, the program will still complete its analysis. To remark that the program only processes micrographs that have not been previously analyzed: in other words, if the directory for processing already contains the results of a previous analysis from one micrograph, this micrograph will not be analyzed again, instead the results already available will be displayed in the GUI.
  
-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 ===== ===== Test Data =====
 +In order to get familiar with the program, here is provided a [[http://​bakerlab.ucsd.edu/​programs/​code/​TestCaseAutoRTM_GLV.tar.gz|Test Dataset]] to download. The compressed archive contains few micrographs of Giardia lamblia virus (GLV) (see Janssen M.E. et al (2015) J. Virol. 89:​1182-94 ​ [[http://​dx.doi.org/​10.1128/​jvi.02745-14]] for details on the virus and the microscopy) and two session files, ''​GLVdataset.ars''​ and ''​GLVdatasetctf4.ars''​ (for using CTFFIND4, only valid on Linux), with all the required settings. To test the program:
 +  * uncompress the archive and go into the directory generated
 +
 +  tar xvfz TestCaseAutoRTM_GLV.tar.gz
 +
 +  * go into the directory generated and launch the program
 +
 +  cd GLV
 +  autortm
 +
 +  * from the Session menu, load one of the session file and then press the button ''​Start monitoring''​.
 +  * inspect the results as displayed after the processing of each micrograph.
 +
 +----
 +===== 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 =====