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

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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_9OfJBdt3NpYsxuQDfFpoYB0UvfZOD6raxiewgWcqM4OvnoPllNSMlWLMspaMHjLt1V7kuPecGxqsrPK9EBDpfxAfaCDC6szSGeB9ij_uEjlBHcQjs3pOOG_1mC8eolnq1DCZJCmKkeUvBC9fQV2MLdt5-vrjE2mh0PnMz_ujnaRMxfkUhC2gYCoo35nTLhh4JmkFAsbkhu_UbiOk8A3TeoMjlTqGas5DnS2xfg4h4C-DNkFGV5sYFR0Rj7ek4N5OrAn6gwIfHPntibALQac_6qDvh9a6d5Qk3m3ww8UMCtCmMl-BOCfDwOV0CWe8D9q-_68l9TpQ/https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fvolume.html%23mask>

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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