Dear chimerax-team, I am looking into a possibility to generate a spherical volume in chimerax that I can then use as a spherical mask for focused 3D classifications and signal subtractions. For my specific need, a sphere would be the ideal shape. So far I managed to generate a surface model using the ‘shape sphere’ command, to place it to the region of interest and resampling it onto the coordinate system of my protein of interest. Is there any possibility to transform the surface model into a (binarized) volume? Best, Lorenz
Dear Lorenz, If I understand correctly, you do not need to convert the sphere surface to a volume. The "volume mask" command uses a surface model to delineate the masking area of your map, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2023, at 2:13 AM, Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear chimerax-team,
I am looking into a possibility to generate a spherical volume in chimerax that I can then use as a spherical mask for focused 3D classifications and signal subtractions. For my specific need, a sphere would be the ideal shape. So far I managed to generate a surface model using the ‘shape sphere’ command, to place it to the region of interest and resampling it onto the coordinate system of my protein of interest. Is there any possibility to transform the surface model into a (binarized) volume?
Best, Lorenz
Hi Lorenz, A very quick and dirty way of getting a ~sphere in ChimeraX is using molmap on a single atom (can be from any pdb), e.g. something like this: molmap XXX YYY where XXX is your atom selection and YYY will increase the radius of your sphere. This sphere can then be moved and resampled onto your grid and turned into a mask with soft edge. Best, Moritz From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Wednesday, August 9, 2023 at 12:31 PM To: Grundmann,Lorenz Emanuel <lorenz.grundmann@imp.ac.at> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: Spherical mask External Email - Use Caution Dear Lorenz, If I understand correctly, you do not need to convert the sphere surface to a volume. The "volume mask" command uses a surface model to delineate the masking area of your map, see: <https://secure-web.cisco.com/1tdF9Kj_SlYdRk_9OfJBdt3NpYsxuQDfFpoYB0UvfZOD6ra...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2023, at 2:13 AM, Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear chimerax-team,
I am looking into a possibility to generate a spherical volume in chimerax that I can then use as a spherical mask for focused 3D classifications and signal subtractions. For my specific need, a sphere would be the ideal shape. So far I managed to generate a surface model using the ‘shape sphere’ command, to place it to the region of interest and resampling it onto the coordinate system of my protein of interest. Is there any possibility to transform the surface model into a (binarized) volume?
Best, Lorenz
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Yet another related approach is that the Map Eraser tool erases within a sphere that you can easily size/position interactively: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2023, at 2:13 AM, Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear chimerax-team,
I am looking into a possibility to generate a spherical volume in chimerax that I can then use as a spherical mask for focused 3D classifications and signal subtractions. For my specific need, a sphere would be the ideal shape. So far I managed to generate a surface model using the ‘shape sphere’ command, to place it to the region of interest and resampling it onto the coordinate system of my protein of interest. Is there any possibility to transform the surface model into a (binarized) volume?
Best, Lorenz
Dear Elaine and dear Moritz, Thank you very much for your suggestions! Especially the hack to just use molmap and a single atom is such a fun exploit. I eventually found a solution and it is also easy. As you can use this to generate masks in various fun shapes, I will share it here. 1. Create a sphere using ‘shape sphere X’ X being the radius (In order to generate your favorite geometric shape of choice, please see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html). 2. Move the surface model via ‘move model’ functionality. 3. Create a map with values of 1 bounded by your surface via ‘volume onesmask #Y onGrid #Z”. Y being the volume to be masked and Z your surface model (see https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask). Now you have a binarized volume to be used as a mask after adding a soft mask. Best, Lorenz ……………………………….. Lorenz Grundmann PhD Student M +43677/64603163 [Icon Description automatically generated]<https://twitter.com/GrundmannLorenz> lorenz.grundmann@imp.ac.at<mailto:lorenz.grundmann@imp.ac.at> www.imp.ac.at<http://www.imp.ac.at/> IMP Research Institute of Molecular Pathology Campus-Vienna-BioCenter 1 1030 Vienna, Austria Part of Vienna BioCenter From: Elaine Meng <meng@cgl.ucsf.edu> Date: Wednesday, 9. August 2023 at 19:56 To: Grundmann,Lorenz Emanuel <lorenz.grundmann@imp.ac.at> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Spherical mask Yet another related approach is that the Map Eraser tool erases within a sphere that you can easily size/position interactively: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2023, at 2:13 AM, Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear chimerax-team,
I am looking into a possibility to generate a spherical volume in chimerax that I can then use as a spherical mask for focused 3D classifications and signal subtractions. For my specific need, a sphere would be the ideal shape. So far I managed to generate a surface model using the ‘shape sphere’ command, to place it to the region of interest and resampling it onto the coordinate system of my protein of interest. Is there any possibility to transform the surface model into a (binarized) volume?
Best, Lorenz
participants (3)
-
Elaine Meng -
Grundmann,Lorenz Emanuel -
Hunkeler, Moritz