shape tool in ChimeraX
Hi, Chimera has a “shape” command that I find quite useful. Does ChimeraX have this feature? I could not find it in the online documentation. Thanks, Joel
Hi Joel, Sorry, there is no "shape" command in ChimeraX yet, although we would like to add something like that in the future. Currently ChimeraX does have defining 3D objects with the Bild text format, which is very simple: <http://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html> However, the Bild approach is less convenient in that you must create a separate Bild file and then open it, you cannot change colors after creating the objects, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 12, 2020, at 4:19 AM, Joel Meyerson <jrm2008@med.cornell.edu> wrote:
Hi, Chimera has a “shape” command that I find quite useful. Does ChimeraX have this feature? I could not find it in the online documentation. Thanks, Joel
Hi Elaine, Thanks a lot for the tip about Bild files. I'll experiment with that approach. And that's great to know there's interest in developing something like the "shape" command for ChimeraX. Best, Joel On 4/12/20, 1:29 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: Hi Joel, Sorry, there is no "shape" command in ChimeraX yet, although we would like to add something like that in the future. Currently ChimeraX does have defining 3D objects with the Bild text format, which is very simple: <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > However, the Bild approach is less convenient in that you must create a separate Bild file and then open it, you cannot change colors after creating the objects, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 12, 2020, at 4:19 AM, Joel Meyerson <jrm2008@med.cornell.edu> wrote: > > Hi, > Chimera has a “shape” command that I find quite useful. Does ChimeraX have this feature? I could not find it in the online documentation. > Thanks, > Joel
Hi Joel, The "shape" command has been added to ChimeraX and can make spheres, cylinders, cones, smooth tubes, icosahedrons, ... the same stuff that the Chimera shape command did with the same command syntax. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/shape.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/shape.html> Tom
On Apr 12, 2020, at 12:04 PM, Joel Meyerson wrote:
Hi Elaine, Thanks a lot for the tip about Bild files. I'll experiment with that approach. And that's great to know there's interest in developing something like the "shape" command for ChimeraX.
Best, Joel
On 4/12/20, 1:29 PM, "Elaine Meng" wrote:
Hi Joel, Sorry, there is no "shape" command in ChimeraX yet, although we would like to add something like that in the future. Currently ChimeraX does have defining 3D objects with the Bild text format, which is very simple:
<https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... >
However, the Bild approach is less convenient in that you must create a separate Bild file and then open it, you cannot change colors after creating the objects, etc.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 12, 2020, at 4:19 AM, Joel Meyerson wrote:
Hi, Chimera has a “shape” command that I find quite useful. Does ChimeraX have this feature? I could not find it in the online documentation. Thanks, Joel
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Great stuff. Thanks, Tom. Joel From: Tom Goddard <goddard@sonic.net> Date: Monday, April 20, 2020 at 6:36 PM To: Joel Meyerson <jrm2008@med.cornell.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] shape tool in ChimeraX Hi Joel, The "shape" command has been added to ChimeraX and can make spheres, cylinders, cones, smooth tubes, icosahedrons, ... the same stuff that the Chimera shape command did with the same command syntax. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/shape.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimerax_docs_user_commands_shape.html&d=DwMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=JnYzuUa3E5p4u7qrfPzeZV8LIgMpwauz4WIvX7NJIi8&m=R8lu5UkJGC_1d_XL3hHAq8YY9TEq3QMOrmmdNHlrSqc&s=vthdSp1lCn9qle8ZuS5hCBTr3SltZNf99P6FpQ6G_kg&e=> Tom On Apr 12, 2020, at 12:04 PM, Joel Meyerson wrote: Hi Elaine, Thanks a lot for the tip about Bild files. I'll experiment with that approach. And that's great to know there's interest in developing something like the "shape" command for ChimeraX. Best, Joel On 4/12/20, 1:29 PM, "Elaine Meng" wrote: Hi Joel, Sorry, there is no "shape" command in ChimeraX yet, although we would like to add something like that in the future. Currently ChimeraX does have defining 3D objects with the Bild text format, which is very simple: <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > However, the Bild approach is less convenient in that you must create a separate Bild file and then open it, you cannot change colors after creating the objects, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 12, 2020, at 4:19 AM, Joel Meyerson wrote: Hi, Chimera has a “shape” command that I find quite useful. Does ChimeraX have this feature? I could not find it in the online documentation. Thanks, Joel _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Joel Meyerson -
Tom Goddard