Walkthrough for lattices on vesicles

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This walkthrough shows the approach to process proteins that cover spheroidal vesicles following (approximately) a structured lattice. For demonstration, we use a highly binned tomogram with several viral capsides.


The data has been made available by Florian Schur . This single tomogram is part of the data set used for the paper:

Getting the data

You can download the data through:


Viewing the data

The tomogram is severely binned, so it will probably fit in memory without major problems. We can just use our typical tool to quick check a tomogram.

 dtmshow v17.rec 

Particle cropping

We are interested in cropping the particles between the two layers of each one of the viruses.

In our approach, we will first use a single model to manually input the approximate centers and radiuses of all the viruses. We will use the model type dipoleSet. This model allows to describe each annotated virus as a dipole: we will mark the (approximate) center of the virus as the center property of a dipole. The radius of the virus will be described by an annotation of the north property of the dipole.

Selecting the dipoleSet model

When the model is active, we use the key c to mark the center of the current dipole, and n to mark the north. It will create a semitransparent sphere enclosing the completed dipole.

Selecting a dipole: click on C for the center, then N for the north

Further clicks on c or n will just move the center or the north of the same dipole. In order to click a further dipole, you need to click on enter and "open" the next dipole for clicking. If you forget to click on enter before annotating points on the next vesicle, you'll end up with situation like this:

Wrong input: enter needed to be clicked between vesicles 2 and 3

Here, the user probably clicked on c for vesicle 2 in its real center, then clicked on n for the north point, and then moved to vesicle 3, clicking on c trying to mark the center. As a new dipole was not opened (i.e., the enter key was not pressed) when the vesicle 2 was finished, the center of vesicle 2 got misplaced. When this happens, simply press on h to hide the spheres and click the center of vesicle 2 back in its position. Then, press on enter to start the next vesicle.