[Chimera-users] Fitting structure in rescaled map

[Elaine Meng]

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.