Hi Leyre, Yes you can do it, map cropping is a very common action. You can do it interactively with the mouse/trackpad function "crop volume" -- for example, in the Right Mouse tab of the Toolbar icons across the top, clicking the icon that looks like a cube with an arrow assigns the right mouse button to crop your volume box. See here for pictures and explanations of all the icons in that tab: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> Or you can assign it to other buttons (besides right mouse) with the "mousemode" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> Or instead of assigning a button to do it interactively, you can just use the "volume" command "region" option to specify some sub-part of your volume box. When you use the "crop volume" mouse mode for interactive cropping, it will show commands like that in the Log so that you could learn the commands for scripting purposes. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions> Another option if you already have atoms fitted into the map is to simply hide the map parts that are far from atoms. You can do this with the "volume" command "zone" option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone> There is a Map tab in the Toolbar icons across the top. It contains an icon to do the zone function mentioned above. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/densitymaps.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 29, 2024, at 7:01 AM, Leyre Marin Arraiza via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF ChimeraX,
I have a practical question regarding 3D volume visualization and cropping in ChimeraX.
I have a big 3D density map which includes the densities for several models of different proteins. To facilitate visualization and model building, I would like to crop the density map, so that it includes only two of the models.
Is it possible to crop my density map around those models, to make it a bit smaller and more focused on the areas of interest?
Hope I am explaining myself. Thanks and best regards, Leyre