Boxer manual picking - cianfrocco-lab/Old-school-processing GitHub Wiki

Home > Picking particles > Manual picking with boxer

###Manual picking with boxer

• Launching boxer & picking particles
• Saving particles as particle coordinates
• Viewing particle picks using boxer

###Launching boxer & picking particles

Manual picking with boxer is straightforward given its graphical user interface (GUI).

To open a micrograph, simply provide the micrograph name alongside the boxer command:

$ boxer Frame23.mrc 

This will open three windows:

• A window containing your micrograph (left window below)
• A blank window that will show picked particles (lower right window below)
• Main menu window (upper right window below)

First, you must input a box size for the particles that you will be selecting in the main menu window. To learn more about how to measure the diameter of your sample & picking a box size, read more here. After selecting the box size, make sure the 'Select' button is pressed and then now you can start picking your particles:

You will see the picked particles appear in the extracted particle window.

Tips for using boxer:

• To change the zoom & contrast on the micrograph, middle click using your mouse and a new window will appear. Adjust the scale to zoom in or out, and slide the bars to change the contrast.
• To remove particles that you don't want, you can press the 'Delete' button in the menu and then left click each particle that you want removed. When you are ready to start selecting particles again, make sure re-click the 'Select' button.

###Saving particles

When you are ready to save your particles, you can save the particle coordinates into a text file (.box format):

1. Click: 'Boxes > Save Box DB'
2. Then specify the output file name. It is a good idea to save the .box file as the same name as the micrograph. For instance, if you picked particles from 'Frame23.mrc', then you should save the particles as 'Frame23.box'.
3. After saving the file, you can exit boxer by clicking the 'X' in the top left corner, or going to 'File > Quit'.

###Viewing particle picks using boxer

You can always re-open your particle picks using boxer.

First, open the micrograph of interest:

$ boxer Frame34.mrc

Then, in boxer's main window, go to 'Boxes > Read Box DB'. In the next window, navigate to the .box file that you wish to open.

Important: The scaling must be the same between the .box file and the micrograph. This means that if the .box file came from a binned version of your micrograph, you need to open the binned micrograph. This is because the .box file are X & Y coordinates that need to be scaled depending on the binning (or not) of your micrograph.

If you did not do any processing to your micrographs before picking, then you have nothing to worry about.