Changing cryo-em density map x=voxel size in Chimera
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@mail.missouri.edu Mobile: (573 )-289-9073
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" <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> - OR - (B) "volume" command with the "voxelSize" option, as described here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions> 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 ----- 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@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.
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. Tom
On Mar 15, 2020, at 12:18 PM, Ouadou, Anes (MU-Student) <aomqc@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@mail.missouri.edu <mailto:aomqc@mail.missouri.edu> Mobile: (573 )-289-9073 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
participants (3)
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Elaine Meng -
Ouadou, Anes (MU-Student) -
Tom Goddard