[chimerax-users] Re: Option to convert shape to map?

Hi Vincent, The transparency command works on shapes. If you want the shape without caps, you can specify caps off, but then the walls will be infinitely thin. I think what you want is a transparent cylinder with walls of a finite thickness, in which case you could make two cylinders, use the volume onesmask command to convert them to maps, and then subtract one from the other. You might want to make the one you are subtracting just a little longer than the outer one, so that you don't have a residual cap at one end. Cheers Oli 

On Jan 18, 2024, at 7:09 AM, vincent Chaptal wrote:

Hi,

the shape is a great tool. I was wondering if it is possible to display a hollow cylinder, specifying the start and end radius? Also, I couldn't render the cylinder transparent. Is it possible?

Thank you. Vincent

Le 17/01/2024 à 22:03, Eric Pettersen via ChimeraX-users a écrit :

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Yes, in the "shape" help page, under General Options where it describes "center", clicking on the point-spec link shows "cofr" as one of the possible values.

--Eric

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On Jan 17, 2024, at 1:00 PM, Oliver Clarke mailto:olibclarke@gmail.com> wrote:

That is what I was looking for! Is that in the docs and I missed it? (probably...)

Oli

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On Jan 17, 2024, at 3:56 PM, Eric Pettersen mailto:pett@cgl.ucsf.edu> wrote:

Also: shape cylinder radius 50 height 100 center cofr To center the created shape at the center of rotation.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

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On Jan 17, 2024, at 12:52 PM, Oliver Clarke via ChimeraX-users mailto:chimerax-users@cgl.ucsf.edu> wrote:

Hi Tom,

I usually have the center of rotation visible, using "showpivot true", so it is clear where the center of rotation is. It would be useful I think to have the option to move things to the center of rotation, like in Chimera (because the place I want the mask is not always in the center of the map), but this approach works too!

Cheers Oli

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On Jan 17, 2024, at 3:48 PM, Tom Goddard mailto:goddard@sonic.net> wrote:

Hi Oli,

There is no command in ChimeraX that moves models to the center of rotation like the Chimera "move cofr" command. If the idea is to use the shape command and then place the shape at the center of an existing map (e.g. model #1) then I would suggest using the "center" option of the shape command

shape cylinder radius 50 height 100 center #1

It is not obvious where the center of rotation point is in ChimeraX, for instance it may be on the surface of a displayed map in the center of the view that is not near the center of the map. So I don't think a "move cofr" would do this job very well.

Tom

> On Jan 17, 2024, at 10:54 AM, Oliver Clarke mailto:olibclarke@gmail.com> wrote: > > Relatedly - is there any ChimeraX command line equivalent to "move cofr" in Chimera - to move a designated model to the current center of rotation? > > Cheers > Oli > >> On Jan 17, 2024, at 1:43 PM, Oliver Clarke mailto:olibclarke@gmail.com> wrote: >> >> Perfect thanks Tom - I did not know about the "volume onesmask" command (I looked in the docs but clearly not in the right place!), but that is exactly what I was looking for! >> >> Cheers >> Oli >> >>> On Jan 17, 2024, at 1:39 PM, Tom Goddard mailto:goddard@sonic.net> wrote: >>> >>> Hi Oliver, >>> >>> This is easy to do with the existing "volume onesmask" and "volume falloff" commands. For example >>> >>> open 1080 from emdb >>> shape cylinder radius 50 height 100 >>> volume onesmask #2 ongrid #1 >>> volume falloff #3 >>> >>> I don't think it is worthwhile to cram all the onesmask and falloff options into the shape command. You might also use the "volume gaussian" command instead of the "volume falloff" command to soften the edges. The volume falloff command will not modifiy the ones region, only the zeros outside the boundary, while the volume gaussian command will modify inside and outside the mask. >>> >>> Tom >>> >>> >>>> On Jan 17, 2024, at 8:22 AM, Oliver Clarke via ChimeraX-users mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>> >>>> Hi, >>>> >>>> Would it be possible in a future release to add an option to the "shape" command to output the shape as a map (filled with 1s inside the shape, zeroes outside, maybe with an optional soft edge and an ongrid option)? >>>> >>>> This would be very convenient for making simple geometrical masks for cryoEM (e.g soft cylindrical masks for classification within a nanodisc). >>>> >>>> I currently do this using "shape cylinder", use the cylinder to mask the map, and then gaussian filter the resulting masked map to the point where I can choose a threshold that conforms to the shape, but having a way to do the same thing more directly would be very nice to have. >>>> >>>> Cheers >>>> Oli >>>> _______________________________________________ >>>> ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu >>>> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu >>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>> >>> >> > >

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