Hi Vijay, The meshmol command from Chimera which converts a surface mesh from wire edges to cylinder edges (making a fake molecule) is not yet in ChimeraX. But I can add it pretty easily, maybe tomorrow if time permits. Tom Icosahedral cage shown with wires and with meshmol cylinders
On Nov 18, 2021, at 2:38 PM, Vijay Reddy <reddyv@scripps.edu> wrote:
Hi Tom,
Greetings! Hope are staying safe and healthy.
I am finally transitioning to chimeraX.
Could you please tell me what is the equivalent of
the chimera command “meshmol #26 6” in chimeraX
Many thanks, Vijay
Many thanks Tom, I created an icosahedron using “shape icosahedron…” command. I would like to get the edges highlighted using the meshmol command that I used before in Chimera. Please drop me an e-mail when it is available in ChimeraX. Best regards, Vijay -- From: Tom Goddard <goddard@sonic.net> Date: Thursday, November 18, 2021 at 10:41 PM To: Vijay Reddy <reddyv@scripps.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: meshmol in chimeraX Hi Vijay, The meshmol command from Chimera which converts a surface mesh from wire edges to cylinder edges (making a fake molecule) is not yet in ChimeraX. But I can add it pretty easily, maybe tomorrow if time permits. Tom Icosahedral cage shown with wires and with meshmol cylinders [cid:image001.png@01D7DD1A.2016C3D0] On Nov 18, 2021, at 2:38 PM, Vijay Reddy <reddyv@scripps.edu<mailto:reddyv@scripps.edu>> wrote: Hi Tom, Greetings! Hope are staying safe and healthy. I am finally transitioning to chimeraX. Could you please tell me what is the equivalent of the chimera command “meshmol #26 6” in chimeraX Many thanks, Vijay
Hi Vijay, I added the meshmol command to ChimeraX. It will be in tomorrow's daily build, but not in the 1.3 release we expect to make in one week. For example, to make a marker model with edge radius 1.5 from an icosahedron surface mesh shape icosahedron radius 50 mesh true divisions 15 spherefactor 1 meshmol #1 1.5 By the way, the hkcage command in ChimeraX automatically makes the marker models so you may want to use that instead. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/hkcage.html Tom
On Nov 19, 2021, at 7:50 AM, Vijay Reddy via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Many thanks Tom, I created an icosahedron using “shape icosahedron…” command. I would like to get the edges highlighted using the meshmol command that I used before in Chimera. Please drop me an e-mail when it is available in ChimeraX. Best regards, Vijay
--
Oops! ChimeraX already had the equivalent of the meshmol command but with a different name "marker fromMesh" shape icosahedron radius 50 mesh true divisions 15 spherefactor 1 marker fromMesh #1 edgeRadius 0.5 color pink I have removed the meshmol command. Please use marker fromMesh https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html Tom
On Nov 22, 2021, at 3:30 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Vijay,
I added the meshmol command to ChimeraX. It will be in tomorrow's daily build, but not in the 1.3 release we expect to make in one week. For example, to make a marker model with edge radius 1.5 from an icosahedron surface mesh
shape icosahedron radius 50 mesh true divisions 15 spherefactor 1 meshmol #1 1.5
By the way, the hkcage command in ChimeraX automatically makes the marker models so you may want to use that instead.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/hkcage.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/hkcage.html>
Tom
On Nov 19, 2021, at 7:50 AM, Vijay Reddy via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Many thanks Tom, I created an icosahedron using “shape icosahedron…” command. I would like to get the edges highlighted using the meshmol command that I used before in Chimera. Please drop me an e-mail when it is available in ChimeraX. Best regards, Vijay
--
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participants (2)
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Tom Goddard -
Vijay Reddy