Option to convert shape to map?
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
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 <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 To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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 <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 <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 To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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 <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 <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 <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 To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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 <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 <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 <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 <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 To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 <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 <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 <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 <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 To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
On Jan 17, 2024, at 12:52 PM, Oliver Clarke via ChimeraX-users <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
On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 <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 <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 <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 <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 To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
That is what I was looking for! Is that in the docs and I missed it? (probably...) Oli
On Jan 17, 2024, at 3:56 PM, Eric Pettersen <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
On Jan 17, 2024, at 12:52 PM, Oliver Clarke via ChimeraX-users <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
On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 <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 <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 <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 <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 > To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >
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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
On Jan 17, 2024, at 1:00 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
That is what I was looking for! Is that in the docs and I missed it? (probably...)
Oli
On Jan 17, 2024, at 3:56 PM, Eric Pettersen <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
On Jan 17, 2024, at 12:52 PM, Oliver Clarke via ChimeraX-users <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
On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 <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 <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 <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 <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 >> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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 :
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
On Jan 17, 2024, at 1:00 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
That is what I was looking for! Is that in the docs and I missed it? (probably...)
Oli
On Jan 17, 2024, at 3:56 PM, Eric Pettersen <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
On Jan 17, 2024, at 12:52 PM, Oliver Clarke via ChimeraX-users <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
On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 <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 > <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 <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 >>> <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 >>> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu >>> Archives: >>> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> >> >
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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
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 <vincent.chaptal@ibcp.fr> 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 :
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
On Jan 17, 2024, at 1:00 PM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
That is what I was looking for! Is that in the docs and I missed it? (probably...)
Oli
On Jan 17, 2024, at 3:56 PM, Eric Pettersen <pett@cgl.ucsf.edu <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
On Jan 17, 2024, at 12:52 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu <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
On Jan 17, 2024, at 3:48 PM, Tom Goddard <goddard@sonic.net <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 <olibclarke@gmail.com <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 <olibclarke@gmail.com <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 <goddard@sonic.net <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 <chimerax-users@cgl.ucsf.edu <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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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr <http://www.appicom.cnrs.fr/> http://mmsb.cnrs.fr/en/
Thanks Oli. it looks nice. I'll formalize it so that it's available in detbelt. Cheers Vincent Le 18/01/2024 à 13:17, Oliver Clarke a écrit :
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 PastedGraphic-1.pngPastedGraphic-2.png
On Jan 18, 2024, at 7:09 AM, vincent Chaptal <vincent.chaptal@ibcp.fr> 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 :
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
On Jan 17, 2024, at 1:00 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
That is what I was looking for! Is that in the docs and I missed it? (probably...)
Oli
On Jan 17, 2024, at 3:56 PM, Eric Pettersen <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
On Jan 17, 2024, at 12:52 PM, Oliver Clarke via ChimeraX-users <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
> On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 >> <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 >>> <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 <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 <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 >>>>> To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu >>>>> Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>>> >>>> >>> >> >> >
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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
Would it be possible to add a "move cofr" command to chimerax at some point? We use this frequently in Chimera to move an atomic model to a precise point in a map (when we often don't have any other models in there to align to). I know one can do this graphically using "translate selected models", but it is much easier and more precise in my experience to position the center of rotation (using the showPivot indicator) where I want to be, and then move the model to the center of rotation. Cheers Oli
On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 <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 <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 <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 <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 To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Vincent, You can make a cylinder with inner radius 50 and outer radius 70 using the slab option of “shape cylinder”. shape cylinder radius 50 height 100 caps false slab 0,20 Transparency works fine “transparency #1 80”. And you can make a mask from this thick cylinder ("volume onesmask #1 ongrid #2”). Documentation for shape cylinder command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/shape.html#cylinder Tom
On Jan 18, 2024, at 4:09 AM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> 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 :
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
On Jan 17, 2024, at 1:00 PM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
That is what I was looking for! Is that in the docs and I missed it? (probably...)
Oli
On Jan 17, 2024, at 3:56 PM, Eric Pettersen <pett@cgl.ucsf.edu <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
On Jan 17, 2024, at 12:52 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu <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
On Jan 17, 2024, at 3:48 PM, Tom Goddard <goddard@sonic.net <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 <olibclarke@gmail.com <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 <olibclarke@gmail.com <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 <goddard@sonic.net <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 <chimerax-users@cgl.ucsf.edu <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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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr <http://www.appicom.cnrs.fr/> http://mmsb.cnrs.fr/en/
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Hi Oli, I don’t quite understand how this is useful. If you position a model at the center of rotation don’t you also have to rotate it to a sensible orientation. How do you do the rotation? Are you trying to do a fit in a map? I agree the current way that is done in ChimeraX where you have to move the map by hand is cumbersome. Maybe instead an option to the fitmap command to first move the model to the center of rotation and then optimize the fit (possibly with a rotational search) would better get at what are trying to do. Tom
On Jan 18, 2024, at 3:14 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Would it be possible to add a "move cofr" command to chimerax at some point? We use this frequently in Chimera to move an atomic model to a precise point in a map (when we often don't have any other models in there to align to).
I know one can do this graphically using "translate selected models", but it is much easier and more precise in my experience to position the center of rotation (using the showPivot indicator) where I want to be, and then move the model to the center of rotation.
Cheers Oli
On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 <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 <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 <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 <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 To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Hi Oli, Ok I added a "move cofr <models-spec>" command, for example, move cofr #2 Syntax is slightly different than in Chimera which required a "models" keyword. Also the distance and frames options seen in the Chimera command are not in ChimeraX. If multiple models are specified they are moved rigidly as a group so that their bounding box center (displayed parts only) is moved to the current center of rotation. Tom
From: Oliver Clarke <olibclarke@gmail.com> Subject: Re: [ChimeraX] #14408: Add command to move models to center of rotation Date: January 18, 2024 at 4:31:57 PM PST To: ChimeraX-bugs@cgl.ucsf.edu Cc: goddard@cgl.ucsf.edu
Yes an option for fitmap could do the trick, although a separate move cofr command would be more flexible in my opinion.
In Chimera, I would generally move the cofr where I want to position the model, “move cofr” to move it, then I would either use fitmap with global search (“search 100 radius 5”) or quickly manually reorient (which I do about equally as often). It might sound cumbersome but feels pretty quick and intuitive!
Either way, I find being able to reposition a model to the center of rotation useful.
Cheers Oli
On Jan 18, 2024, at 4:12 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oli,
I don’t quite understand how this is useful. If you position a model at the center of rotation don’t you also have to rotate it to a sensible orientation. How do you do the rotation? Are you trying to do a fit in a map? I agree the current way that is done in ChimeraX where you have to move the map by hand is cumbersome. Maybe instead an option to the fitmap command to first move the model to the center of rotation and then optimize the fit (possibly with a rotational search) would better get at what are trying to do.
Tom
On Jan 18, 2024, at 3:14 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Would it be possible to add a "move cofr" command to chimerax at some point? We use this frequently in Chimera to move an atomic model to a precise point in a map (when we often don't have any other models in there to align to).
I know one can do this graphically using "translate selected models", but it is much easier and more precise in my experience to position the center of rotation (using the showPivot indicator) where I want to be, and then move the model to the center of rotation.
Cheers Oli
On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 <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 <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 <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 <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 > To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >
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Wonderful, thanks so much Tom! Oli
On Jan 19, 2024, at 4:16 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oli,
Ok I added a "move cofr <models-spec>" command, for example,
move cofr #2
Syntax is slightly different than in Chimera which required a "models" keyword. Also the distance and frames options seen in the Chimera command are not in ChimeraX. If multiple models are specified they are moved rigidly as a group so that their bounding box center (displayed parts only) is moved to the current center of rotation.
Tom
From: Oliver Clarke <olibclarke@gmail.com> Subject: Re: [ChimeraX] #14408: Add command to move models to center of rotation Date: January 18, 2024 at 4:31:57 PM PST To: ChimeraX-bugs@cgl.ucsf.edu Cc: goddard@cgl.ucsf.edu
Yes an option for fitmap could do the trick, although a separate move cofr command would be more flexible in my opinion.
In Chimera, I would generally move the cofr where I want to position the model, “move cofr” to move it, then I would either use fitmap with global search (“search 100 radius 5”) or quickly manually reorient (which I do about equally as often). It might sound cumbersome but feels pretty quick and intuitive!
Either way, I find being able to reposition a model to the center of rotation useful.
Cheers Oli
On Jan 18, 2024, at 4:12 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oli,
I don’t quite understand how this is useful. If you position a model at the center of rotation don’t you also have to rotate it to a sensible orientation. How do you do the rotation? Are you trying to do a fit in a map? I agree the current way that is done in ChimeraX where you have to move the map by hand is cumbersome. Maybe instead an option to the fitmap command to first move the model to the center of rotation and then optimize the fit (possibly with a rotational search) would better get at what are trying to do.
Tom
On Jan 18, 2024, at 3:14 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Would it be possible to add a "move cofr" command to chimerax at some point? We use this frequently in Chimera to move an atomic model to a precise point in a map (when we often don't have any other models in there to align to).
I know one can do this graphically using "translate selected models", but it is much easier and more precise in my experience to position the center of rotation (using the showPivot indicator) where I want to be, and then move the model to the center of rotation.
Cheers Oli
On Jan 17, 2024, at 3:48 PM, Tom Goddard <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 <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 <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 <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 <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 >> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >
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participants (4)
-
Eric Pettersen -
Oliver Clarke -
Tom Goddard -
vincent Chaptal