[Chimera-users] Fitting structure in rescaled map

Ahmad Khalifa underoath006 at gmail.com
Wed Sep 23 13:42:33 PDT 2020

Thank you. I have a follow up question. How does vop resample change the
voxel size and box size? Does it change the map scale?

I've been scaling my maps using relion_image_handler, which oversamples or
downsamples the map (changing the voxel size), while maintaining the box
size (doesn't change the overall map scale). How can I use vop scale to do
the same?!

On Mon, Apr 27, 2020 at 9:33 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ahmad,
> The atomic models are in angstrom coordinates, so yes, they are to scale.
> It is probably the map that is out of scale since it was shrunk.   There
> are two kinds of downscaling, actually shrinking the size, or just scaling
> down the density values without shrinking the size.  Maybe you did the
> first one when you really wanted to do the second one.
> Adjusting voxel size (shrinking or enlarging) can be done in Volume
> Viewer, Features... Coordinates
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale>
> ... or "volume" command with "voxelSize" option
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions
> >
> Adjusting density values without changing the size can be done with "vop
> scale"
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale>
> I hope this helps,
> ELaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Apr 26, 2020, at 4:58 PM, Ahmad Khalifa <underoath006 at gmail.com>
> wrote:
> >
> > Hello,
> > How to fit an atomic model after downscaling my map (map shrinks)? Are
> atomic models built to scale?!
> > Regards.
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