Hello ! In the effort to create a more integrated pipeline with vastly used 3d software (I use mainly C4D and modo) is there a way to export animation from chimera in a format that other software can interpret. To make an example. If I wiggle a molecule in chimera, can I export the animation in a format that does not lot this info ? And eventually are there plan to create this feature in chimeraX ? Giorgio
On Mar 6, 2017, at 6:21 AM, Giorgio Luciano giorgio.luciano@gmail.com wrote:
Hello ! In the effort to create a more integrated pipeline with vastly used 3d software (I use mainly C4D and modo) is there a way to export animation from chimera in a format that other software can interpret. To make an example. If I wiggle a molecule in chimera, can I export the animation in a format that does not lot this info ? And eventually are there plan to create this feature in chimeraX ? Giorgio
Hi Giorgio, Chimera supports several export formats, see “File… Export Scene” in the menu or the “export” command.
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html
However, these are for individual conformations, not for a whole animation, so you’d have to export at each step.
Although ChimeraX is in early development, currently the “save” command formats include STL and X3D. The command “save formats” lists all the formats that can be saved.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html
These may be subject to the same limitations mentioned in the Chimera manual links above.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Thanks for the info and sorry for my late reply. I generally export using x3d what I was thinking about is, how can someone export the single model for an animation ? As an example if I make wiggle a molecule play (wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 200 ) may I export in batch the molecules for the single frame ? Any help will be greatly appreciated :)
Il giorno lun 6 mar 2017 alle ore 18:57 Elaine Meng meng@cgl.ucsf.edu ha scritto:
On Mar 6, 2017, at 6:21 AM, Giorgio Luciano giorgio.luciano@gmail.com
wrote:
Hello ! In the effort to create a more integrated pipeline with vastly
used 3d software (I use mainly C4D and modo) is there a way to export animation from chimera in a format that other software can interpret. To make an example. If I wiggle a molecule in chimera, can I export the animation in a format that does not lot this info ? And eventually are there plan to create this feature in chimeraX ?
Giorgio
Hi Giorgio, Chimera supports several export formats, see “File… Export Scene” in the menu or the “export” command.
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html
However, these are for individual conformations, not for a whole animation, so you’d have to export at each step.
Although ChimeraX is in early development, currently the “save” command formats include STL and X3D. The command “save formats” lists all the formats that can be saved.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html
These may be subject to the same limitations mentioned in the Chimera manual links above.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Hi Giorgio, You would still have to use the “export” command that exports one file at a time, but it can be run at every frame by combining it with the “perframe” command.
For example, in Chimera the following (should be all one line even though the Mail app may break it up):
perframe "export ~/temp/$1.x3d" zero 2; play wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 50; wait 50; ~perframe
…where ~/temp is a directory that already exists, will make files 01.x3d …. 50.x3d in that directory.
In ChimeraX, there is a “perframe” command and “save” to export X3D, but no “play wiggle” command.
http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 9, 2017, at 11:44 AM, Giorgio Luciano giorgio.luciano@gmail.com wrote:
Thanks for the info and sorry for my late reply. I generally export using x3d what I was thinking about is, how can someone export the single model for an animation ? As an example if I make wiggle a molecule play (wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 200 ) may I export in batch the molecules for the single frame ? Any help will be greatly appreciated :)
Hello Elaine, and thanks as always for your reply. I will give it a try tomorrow. I hope I will get a good animation and I will also post the making of. Giorgio
Il giorno gio 9 mar 2017 alle ore 21:53 Elaine Meng meng@cgl.ucsf.edu ha scritto:
Hi Giorgio, You would still have to use the “export” command that exports one file at a time, but it can be run at every frame by combining it with the “perframe” command.
For example, in Chimera the following (should be all one line even though the Mail app may break it up):
perframe "export ~/temp/$1.x3d" zero 2; play wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 50; wait 50; ~perframe
…where ~/temp is a directory that already exists, will make files 01.x3d …. 50.x3d in that directory.
In ChimeraX, there is a “perframe” command and “save” to export X3D, but no “play wiggle” command.
http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 9, 2017, at 11:44 AM, Giorgio Luciano giorgio.luciano@gmail.com
wrote:
Thanks for the info and sorry for my late reply. I generally export
using x3d what I was thinking about is, how can someone export the single model for an animation ? As an example if I make wiggle a molecule play (wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 200 ) may I export in batch the molecules for the single frame ?
Any help will be greatly appreciated :)
Dear All, I'm preparing mockups of the UI of chimera since I need to prepare some printed tutorials materials. First of all I will be glad to share them and I was also thinking that I can prepare some icons for the most common functions. How may I contribute them ? Giorgio
Hi Giorgio, Were these for Chimera or ChimeraX (you sent mail to both lists)? Either way, we would be happy to link to any tutorial you prepare. If you want to send a PDF instead, we would try to put it up somewhere. As for the icons, I’m guessing we’re talking about a ChimeraX toolbar? If so, we would certainly try to use them if you sent them. You could send them to me. Short descriptions of what they’re supposed to do would help. :-)
—Eric
On Apr 28, 2017, at 2:46 AM, Giorgio Luciano giorgio.luciano@gmail.com wrote:
Dear All, I'm preparing mockups of the UI of chimera since I need to prepare some printed tutorials materials. First of all I will be glad to share them and I was also thinking that I can prepare some icons for the most common functions. How may I contribute them ? Giorgio _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Eric Pettersen -
Giorgio Luciano