[Chimera-users] scale problem

Yaowang Li liyaowang2911 at gmail.com
Tue Nov 24 07:17:14 PST 2015

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.



On Mon, Nov 23, 2015 at 7:50 PM, Tom Goddard <goddard at 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.
> Tom
> 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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