[Chimera-users] Changing cryo-em density map x=voxel size in Chimera

Tom Goddard goddard at sonic.net
Mon Mar 16 12:19:20 PDT 2020

Hi Anes,

   If you get an experimental EM map from say the EM Databank it already has the correct voxel size (ie grid spacing) and will not have voxel size 1.  Usually they choose a voxel size about 1/3 of map resolution.  If this is your situation you don't want to change the voxel size in Chimera -- that simply rescales the map and then alpha helices won't be the correct size in Angstroms.  Instead you want to resample the map on a grid that has voxel size 1.0 Angstrom.  This is a pain to do in Chimera but is very easy in our newer program ChimeraX.

  In ChimeraX you can do it with the "volume resample" command, for example,

	open 20309 from emdb
	vol resample #1 spacing 1.0
	save newmap.mrc model #2

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#resample <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#resample>

If you resample high resolution maps with voxel size say 0.6 Angstroms you may get somewhat noisy appearance on a 1.0 Angstrom grid and you may want to smooth the map before resampling with the "volume gaussian" command.


> On Mar 15, 2020, at 12:18 PM, Ouadou, Anes (MU-Student) <aomqc at mail.missouri.edu> wrote:
> Hello,
> I am using cryo-em density maps to create a deep learning model that detects C-alpha atoms. the model I trained uses maps with voxel size of 1x1x1 A. Experimental maps come in different voxel sizes. I found that I can change the voxel size using the option "model-spec". However, I looked everywhere in Chimera menu bar but could not find "model-spec". can you please show me where to find it. I am also open to any other  suggestion to change voxel size.
> Regards
> Anes Ouadou    
> CS PhD Student    
> University of Missouri-Columbia
> aomqc at mail.missouri.edu <mailto:aomqc at mail.missouri.edu>    
> Mobile: (573 )-289-9073
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