How to determine position of block

We need to use UCSF Chimera. If you are using Chimera v1.15, download https://github.com/homurachan/Block-based-recontruction/blob/master/VolumeEraser.zip , which is a small modification by me.

Unzip all files onto "Chimera 1.15 install folder\share". In ubuntu, the general install folder is located on "~/.local/UCSF-Chimera64-1.15".

Open the map that you want to determine position of blocks. Then use "Volume Eraser", like this below: Check whether "Origin Index" or "Voxel size" is correct.

After erase, you can open the "position_for_BBR.txt", which like this.

The true coordinate of block center is:

X = X / Voxel_Size + Origin_Index

Y = Y / Voxel_Size + Origin_Index

Z = Z / Voxel_Size + Origin_Index

In our case, X = -28.7 / 1.4 + 112 = 91.5, and so on.

Now these coordinates can be directly used in "X/Y/Z position of reconstruction" shown below.

Determination of radius of block can be done by the radius in Volume Eraser divided by Voxel_Size. Adjust radius to cover all target subunit inside block.

Your block size should always be significant larger than what you really want to reconstruct.