[Chimera-users] scale problem

Tom Goddard goddard at sonic.net
Mon Nov 23 10:50:42 PST 2015

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.


> On 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

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