This tab generally helps with managing the manual annotation of your particles with Imod.

Specifically, this tab served for picking the ‘seeds’ particles needed for the later “expand” process. In addition, this tab can also be used for the initial reference generation if you don’t have a template yet.

The entire picking principle is based on the *stalkInit* program in PEET. If you are not familiar with what this is, check this example or https://bio3d.colorado.edu/RML_2017/2017_IMOD_PEET_Workshop/Lectures/ModelingAids.pdf

In conclusion, this tab can be used for the following scenarios/applications:

1. Lattice-like particles: picking ‘seed’ particles
2. scattered particles (ribosomes or glycoproteins, etc.)

Our tutorial will only focus on the 1st applications (lattice-like particles).

Inputs needed before running:

1. A user-created folder containing the reconstructed tomograms that will be used for the sub-tomogram average.

   For examples:

   • Create a folder called tomograms under the Manual folder (Manual/tomograms), then soft link all the reconstructed tomograms under Recon/eTomo/TS_xx folders (typically binned with file types as .mrc or .rec) results from the reconstruction folder.

     For example, you can do something as follows:

     ### Customize the bash code for your own setting ###
     mkdir Manual/tomograms; cd Manual/tomograms
     ln -s ../../Recon/eTomo/*/*.rec ./
     

   • Generally, user likes to get the contrast improved before picking. For example, if you are using IsoNet, you can also use the deconv folder which contains all the deconvolved tomograms as input here for manual picking (please also check at the bottom for a note if using denoising maps)

Output you will get:

Root directory

— ManualPick:

— stalkInit_prep: (*.mrc/rec, *_side.mod, *_top.mod, *_bottom.mod) Directory storing particle picking results required for stalkInit. All the operations resulting from the “Top”, “Bottom”, “Side” and “Combine All” functions will be saved here.

• TomoNet only recognizes mod files with the following name conventions: *_side.mod or *_top.mod or *_bottom.mod. Otherwise, it cannot be detected. Therefore, make sure to name your files following the above format.

— initParams: The directory will store 4 new initial alignment files per tomogram from stalkInit results.

1. One *.mod that stores the coordinates of the center for each particle.
2. One *_initMOTL.csv that stores the corresponding initial translation and rotation information.
3. One *_RotAxes.csv that stores the particle Y-axis information.
4. One .mrc/.rec file will be used for the STA. (Note: If you want to use other maps to replace the one you used for initial picking, then just delete this link file and make the new link file)

Below is the GUI used for manual particle picking.

Fig. 4: Particle picking GUI

Click on the browser button for the “Map for Pick” folder. Choose the Manual/tomograms folder and the cells should populate like in Fig. 4.

• Double-click “Top” to open up 3dmod to pick the top particles