[chimerax-users] Fit crystal structure into mrc

[Tom Goddard]

Hi Shiqing,

If you want to scale your marker positions you can do it with a bit of Python typed in the ChimeraX Python shell, menu Tools / General / Shell.  I selected my markers "select #2" then scaled their coordinates by a factor of 1.5 with

from chimerax.markers import selected_markers
m = selected_markers(session)
m.coords = 1.5 * m.coords

  Tom


> On Jun 29, 2021, at 5:06 PM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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! 
> 
> 
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