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eman2:e2tomo_new [2025/08/05 00:19] – created steveludtkeeman2:e2tomo_new [2025/08/05 00:22] (current) – steveludtke
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   * The actual fraction of particle kept should be around (--keep)^3. That is, when --keep=.9, it removes the worst 10% 3D particles, 10% 2D subtilt with the worst score, and 10% of subtilt with the largest drift.    * The actual fraction of particle kept should be around (--keep)^3. That is, when --keep=.9, it removes the worst 10% 3D particles, 10% 2D subtilt with the worst score, and 10% of subtilt with the largest drift. 
  
- {{http://blake.bcm.edu/dl/EMAN2/avg_compare.png| Averaged map comparison |width=600}}+ {{https://blake.bcm.edu/dl/EMAN2/avg_compare.png}}
  
 With default options, the tutorial dataset should be able to get to ~7.5Å resolution. While the reported number is lower, the features in the resulting map are about as good as EMD-11654. With default options, the tutorial dataset should be able to get to ~7.5Å resolution. While the reported number is lower, the features in the resulting map are about as good as EMD-11654.
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 It will take a while to load all metadata, and plot the trajectory of each particle on each tilt image in each tomogram.  It will take a while to load all metadata, and plot the trajectory of each particle on each tilt image in each tomogram. 
  
- {{http://blake.bcm.edu/dl/EMAN2/ptcl_traj.png| Particle trajectory in tilt image |width=600}}+ {{https://blake.bcm.edu/dl/EMAN2/ptcl_traj.png}}
  
 In the top panel, the blue curve represents the average score of all 2D particles in that tilt, and the red curve represents the average distance of the subtilt motion with respect to the alignment of the 3D particle. The quiver plot below shows the trajectory of each individual particle, colored by its alignment score.  In the top panel, the blue curve represents the average score of all 2D particles in that tilt, and the red curve represents the average distance of the subtilt motion with respect to the alignment of the 3D particle. The quiver plot below shows the trajectory of each individual particle, colored by its alignment score. 
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 </code> </code>
  
- {{http://blake.bcm.edu/dl/EMAN2/conf_change1.gif| Ribosome motion 1 |height=250}}{{http://blake.bcm.edu/dl/EMAN2/conf_change.gif| Ribosome motion 2|height=250}}+ {{https://blake.bcm.edu/dl/EMAN2/conf_change1.gif}}{{https://blake.bcm.edu/dl/EMAN2/conf_change.gif}}
  
 Note that since we want to look at the motion of the masked domain within the coordinates of the original refinement, here use the old aliptcls2d.lst file. If the goal is to visualize the motion of other parts of the protein with the focused part fixed, use the newer aliptcls2d file. The program will output two 3D map stacks corresponding to the trajectories of the first two eigenvectors. They can be filtered/masked manually with e2proc3d.py before visualization. Note that since we want to look at the motion of the masked domain within the coordinates of the original refinement, here use the old aliptcls2d.lst file. If the goal is to visualize the motion of other parts of the protein with the focused part fixed, use the newer aliptcls2d file. The program will output two 3D map stacks corresponding to the trajectories of the first two eigenvectors. They can be filtered/masked manually with e2proc3d.py before visualization.
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 Here is an example of initial model generation from a dataset of microtubule-shaped particles from tomograms of flagella. The program can classify the particles generate the initial model of microtubule doublet and the central pair simultaneously.  Here is an example of initial model generation from a dataset of microtubule-shaped particles from tomograms of flagella. The program can classify the particles generate the initial model of microtubule doublet and the central pair simultaneously. 
  
- {{http://blake.bcm.edu/dl/EMAN2/initmodel0.gif| initial model class 0|height=250}}{{http://blake.bcm.edu/dl/EMAN2/initmodel1.gif| initial model class 1|height=250}}+ {{https://blake.bcm.edu/dl/EMAN2/initmodel0.gif}}{{https://blake.bcm.edu/dl/EMAN2/initmodel1.gif}}
  
 The final output can be found in sptsgd_xx/output_clsx.hdf, and the intermediate maps can be found in sptsgd_xx/output_all_clsx.hdf. Note that not all particles are used in the initial model generation, so there won't be the class assignment of the particles. To get that, run the multi-model refinement with the output maps as references.  The final output can be found in sptsgd_xx/output_clsx.hdf, and the intermediate maps can be found in sptsgd_xx/output_all_clsx.hdf. Note that not all particles are used in the initial model generation, so there won't be the class assignment of the particles. To get that, run the multi-model refinement with the output maps as references. 
  
eman2/e2tomo_new.txt · Last modified: by steveludtke