Hi
I've been using UCSF Chimera and recently encountered ChimeraX -- I really like the modern look and feel!
One feature I cannot find in the X version, though, is editing the attributes of an MSMS surface model, where I was able to disable (make 'false') the 'show disjoint surfaces' setting, in the original version.
Most of the time dealing with models I don't need it, but sometimes I like to 3D print molecular models to really get a 'grip' on the models, and that feature of not showing disjoint surfaces has been useful to remove internal 'bubbles', which I learned about through this posting: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html . If internal bubbles are not removed, they waste printing material and increase printing time.
Is there any way to disable showing disjoint surfaces, or otherwise achieve a similar goal in the X version? Thanks!
Best, Sungwook
Hi Sungwook,
You can avoid the internal surface bubbles in ChimeraX using the surface command "visiblePatches 1" option,
open 7exf surface #1 visiblePatches 1 save 7exf_chain_A.stl model #1.2
I don't see how this saves material when making a 3D print since the print will be solid if there are no interior bubbles. But I agree it will print faster on a filament printer since the toolpaths will be simpler since there are no holes to dodge.
Tom
On Dec 5, 2022, at 7:14 PM, Sungwook Woo via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi
I've been using UCSF Chimera and recently encountered ChimeraX -- I really like the modern look and feel!
One feature I cannot find in the X version, though, is editing the attributes of an MSMS surface model, where I was able to disable (make 'false') the 'show disjoint surfaces' setting, in the original version.
Most of the time dealing with models I don't need it, but sometimes I like to 3D print molecular models to really get a 'grip' on the models, and that feature of not showing disjoint surfaces has been useful to remove internal 'bubbles', which I learned about through this posting: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html . If internal bubbles are not removed, they waste printing material and increase printing time.
Is there any way to disable showing disjoint surfaces, or otherwise achieve a similar goal in the X version? Thanks!
Best, Sungwook
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom,
Looks like that does the trick. Thanks a lot!
In 3D printing, one could fill the entire internal space with printing material, but typically one just fills the empty space only with some kind of lattice framework, while printing multiple layers of material for the walls of the outer surface to ensure durability.
If there are structural features *inside*, it seems that there is no way for 3D model slicing softwares to distinguish this reliably (at least I couldn't find one), and they create multiple layers of 'walls' inside as well, ending up wasting time and material. To illustrate the difference, I attach a screenshot of a slicing software (called Ultimaker Cura) where I show a cross section of two copies of the same protein model, one with the trick applied (left) and one without it (right).
Thanks again!
Best, Sungwook
On Wed, Dec 7, 2022 at 3:14 AM Tom Goddard goddard@sonic.net wrote:
Hi Sungwook,
You can avoid the internal surface bubbles in ChimeraX using the surface command "visiblePatches 1" option,
open 7exf surface #1 visiblePatches 1 save 7exf_chain_A.stl model #1.2
I don't see how this saves material when making a 3D print since the print will be solid if there are no interior bubbles. But I agree it will print faster on a filament printer since the toolpaths will be simpler since there are no holes to dodge.
Tom
On Dec 5, 2022, at 7:14 PM, Sungwook Woo via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi
I've been using UCSF Chimera and recently encountered ChimeraX -- I really like the modern look and feel!
One feature I cannot find in the X version, though, is editing the attributes of an MSMS surface model, where I was able to disable (make 'false') the 'show disjoint surfaces' setting, in the original version.
Most of the time dealing with models I don't need it, but sometimes I like to 3D print molecular models to really get a 'grip' on the models, and that feature of not showing disjoint surfaces has been useful to remove internal 'bubbles', which I learned about through this posting: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html . If internal bubbles are not removed, they waste printing material and increase printing time.
Is there any way to disable showing disjoint surfaces, or otherwise achieve a similar goal in the X version? Thanks!
Best, Sungwook
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Sungwook,
Thanks for the explanation and example images. I have printed various molecular surfaces and they are slow to print on filament printers because of the very intricate surface shape, sometimes taking days for larger (15 cm models). It makes sense that removing the unseen interior surface bubbles will speed this up.
Tom
On Dec 6, 2022, at 6:59 PM, Sungwook Woo sungwook.woo@gmail.com wrote:
Hi Tom,
Looks like that does the trick. Thanks a lot!
In 3D printing, one could fill the entire internal space with printing material, but typically one just fills the empty space only with some kind of lattice framework, while printing multiple layers of material for the walls of the outer surface to ensure durability.
If there are structural features *inside*, it seems that there is no way for 3D model slicing softwares to distinguish this reliably (at least I couldn't find one), and they create multiple layers of 'walls' inside as well, ending up wasting time and material. To illustrate the difference, I attach a screenshot of a slicing software (called Ultimaker Cura) where I show a cross section of two copies of the same protein model, one with the trick applied (left) and one without it (right).
Thanks again!
Best, Sungwook
On Wed, Dec 7, 2022 at 3:14 AM Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: Hi Sungwook,
You can avoid the internal surface bubbles in ChimeraX using the surface command "visiblePatches 1" option,
open 7exf surface #1 visiblePatches 1 save 7exf_chain_A.stl model #1.2
I don't see how this saves material when making a 3D print since the print will be solid if there are no interior bubbles. But I agree it will print faster on a filament printer since the toolpaths will be simpler since there are no holes to dodge.
Tom
On Dec 5, 2022, at 7:14 PM, Sungwook Woo via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi
I've been using UCSF Chimera and recently encountered ChimeraX -- I really like the modern look and feel!
One feature I cannot find in the X version, though, is editing the attributes of an MSMS surface model, where I was able to disable (make 'false') the 'show disjoint surfaces' setting, in the original version.
Most of the time dealing with models I don't need it, but sometimes I like to 3D print molecular models to really get a 'grip' on the models, and that feature of not showing disjoint surfaces has been useful to remove internal 'bubbles', which I learned about through this posting: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html . If internal bubbles are not removed, they waste printing material and increase printing time.
Is there any way to disable showing disjoint surfaces, or otherwise achieve a similar goal in the X version? Thanks!
Best, Sungwook
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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participants (2)
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Sungwook Woo -
Tom Goddard