[chimerax-users] Fit crystal structure into mrc

[Elaine Meng]

Hi Shiqing,
Sorry no, there are no "voxels" in an atomic structure.  The scale of an atomic structure is well established, with bond lengths and distances in Angstroms.  So whenever there is a scale mismatch between atomic structure and map, it's essentially always the map model that needs a different voxel size.  Markers are implemented as atomic structures, so even though they aren't "real" atoms, there is no built-in function to change their scale. 

If you color the map before you change its voxel size, do you still need the markers? 

If so, you would probably need to write your own script to calculate new marker coordinates to match the new map dimensions, or simply start over with adding the markers to the map after you change its (the map's) voxel size.

I hope this makes sense.  Sorry for the difficulties,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 29, 2021, at 4:42 PM, SHIQING LIAO via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
> I am trying to build an illustration using marker/color zone. I successfully colored my mrc file. Now, I want to fit a crystal structure I downloaded from pdb into the mrc. But they apparently have different sizes. I tried voxelSize to scale up my mrc, but then all my markers don’t fit with the enlarged mrc. However, voxelSize doesn’t seem to work with the crystal structure (.pdb1) as I got an error message “no volumes specified” when I indeed wrote “volume #5 voxelSize 2”. I am wondering is there any function like voxelSize to scale down the crystal structure? Thank you!