1/11/2024 0 Comments .avi player for macIf fiducials are present, it is not necessary to adjust this number to match the number of fiducials. In most cases, the default npk should be fine. To determine the handedness computationally, try the tutorial here for EMAN2 build after (or EMAN>=2.31). For your own data, it is recommended to confirm the handedness in a few good tomograms, then provide the correct tltax value for the reconstruction of all tomograms. While the program can automatically compute the orientation of the tilt axis, it can lead to a handedness ambiguity in the tomogram (it happens to be correct in the tutorial data). Tomo_0X.hdf is the reconstruction after each iterationĮither specify the correct tltstep if the tilt series is in order from one extreme to the other, or specify the name of a rawtlt file (as produced by serialem/IMOD). Ptclali_0X.hdf has the trace of each landmark throughout the tilt series (they should stay at the center of image all the time if the alignment is good) Samples_0X.hdf shows the top and side view of those landmarks Landmark_0X.txt has the location of the landmarks (which may be fiducials if present) in each iteration You may consider doing this for only one tomogram. ![]() This requires significant additional disk space. This is not required for the remaining steps in the tutorial, but can be used to help understand how the tomogram alignment works.If you wish to look at the intermediate aligned tilt-series and other files, uncheck notmp On a typical workstation reconstruction takes about 4-5 minutes per tomogram.ģD Reconstruction -> Reconstruct TomogramsĪlternatively you can select one or more tilt series from the tiltseries folder For high resolution subtomogram averaging, the raw tilt-series data is used, based on coordinates from particle picking in the downsampled tomograms. Tomograms are not normally reconstructed at full resolution, generally limited to 1k x 1k or 2k x 2k, but the tilt-series are aligned at full resolution. Tiltseries Alignment and Tomogram Reconstruction (20 min)Īlignment of the tilt-series is performed iteratively in conjunction with tomogram reconstruction. Make sure to always include the micrographs folder in the same directory when moving files around. This will create a virtual stack (.lst file) for each tilt series to save disk space. In the cases it does not work, report to us or use the manual way. It works most of the time for micrographs produced by major data collection software (SerialEM, EPU, etc.). In principle, the program will guess which files correspond to one tilt series, as well as their tilt angle, from the naming convention of the files.One alternative and easier way is to have all the micrographs in a folder called micrographs, in the same Generage tiltseries panel, put the micrographs folder in tilt_images, check guess and click Launch. You can build tilt series one by one by selecting all micrographs for one tilt series in tilt_images, specify output and click Launch. If you start from files individual micrographs of the tilt series (after motion correction), use Generate tiltseries to build tilt series from the micrographs. " " (double underscore) is also reserved for describing modified versions of the same file, and should not be used in your original files. It is critical that the filenames not contain any spaces (replace with underscore) or periods (other than the final period used for the file extension). For your own data, you need to know this number. In this step you should enter the correct A/pix in the apix box. Select the files, and make sure importation says copy Make sure the workflow mode is set to "TOMO" not "SPR".While not required, it reduces later errors. You may use "Edit Project" from the Project menu to set default values for the project.Make sure any EMAN2 commands you run are executed from within this folder (not any subfolder). ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |