Dear Tom,
Yeah, it indeed did not change the intensity, I made a mistake, and did not make it clear.
I have a little experience on the this, that is my first time. As I stated, the magnitude of projections is 1.055 A/pixel, so I think the volume size of density map should be 1.055 A/voxel.
A PDB file should be fitted into the density map theoretically I think, while apparently the density map is small compare to PDB. That is why I changed the voxel size to 2.11 A/voxel.
So actually I want to make a confirmation that the grid in the density map whether is 1.055 A/voxel or not. if it is right, I guess something is wrong during the reconstruction.
Regards,
yaowang