[Chimera-users] Fitting structure in rescaled map

[Elaine Meng]

Hi Ahmed,
"vop resample" simply samples the values from your map onto a the grid of a second map, where the points are not exactly at the same positions as the points of the original grid, although their boxes must already overlap in 3D or else all the new values would be zero.  It is done by trilinear interpolation as mentioned in the documentation (links below).  The scale is not changed.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#notes>

For more details on trilinear interpolation, see:
<https://en.wikipedia.org/wiki/Trilinear_interpolation>

However, you can downsample (if I understand that word correctly, it is different than scaling) with "vop bin"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#bin>

I can't think of a command to do the opposite thing (upsample) but I suppose it would be possible by first defining a new grid with smaller spacing using "vop new" and then using that new grid in a "vop resample" command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new>

The "vop scale" function is something different, it scales the density values, not the grid.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 23, 2020, at 1:42 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> 
> 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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