On Nov 24, 2015, at 7:17 AM, Yaowang Li <liyaowang2911@gmail.com> wrote: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,yaowangOn Mon, Nov 23, 2015 at 7:50 PM, Tom Goddard <goddard@sonic.net> wrote:Hi Yaowang,The Chimera Volume Viewer voxel size setting (menu Features / Coordinates) changes the spacing between grid points. It does not change the map intensity values. If it appears to be wrong by a factor of 2 when compared to a PDB file then the voxel size is definitely. I would not just guess that it is a factor of 2 too small — you should find out from whoever did the reconstruction what the correct value is. But if 2.11A is the correct size than your fitting is fine.TomOn Nov 23, 2015, at 1:31 AM, Yaowang Li wrote:Dear all,
I faced a scale problem when I was trying to fit the density map.
A density map was reconstructed from a set of projections which their
magnitude are 1.055A/pixel, with a reference model that is 1.055 A/voxel
and 5 A in resolution. However the pdb file cannot fit into the map
because the map is too much small. So I have to change the voxel size to
double and then can be fitted.
Here I changed the voxel size, I think it changed the scale for the
density. So i just worried about the fitting result.
thanks