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

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 16 09:13:42 PDT 2020

Hi Anes,
The word "model-spec" simply means to specify which model(s) you want a command to work on, for example #3 if your map is open as model #3.  It does not do anything by itself, but can be used with many different commands, as shown in (B) below.

To change voxel size, you could use either of these:

(A) Volume Viewer dialog: in that tool's menu, choose Features... Coordinates.  Then in the dialog you can enter different value(s) for the "Voxel size"

- OR -

(B) "volume" command with the "voxelSize" option, as described here:

 e.g. something like command:

volume #0 voxelSize 0.5

...if your map is open as model #0 and wanted voxel size 0.5  The "#0" part is the model-spec.  It lets you control which map to act on if you had more than one map open and didn't want to change all of them.  If you just want to change all maps (or only one map is open anyway) you can also use something like

volume all voxelSize 0.5

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

> 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.

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