Marking movies in ChimeraX
Begin forwarded message:
Hi, Eric,
Since you are here answering my question, I would like to make use of this opportunity to ask you a question about making movie, I want to make a movie with five different density maps from cryo-EM with different ligands binding in two different conformation, there is no animation interface in ChimeraX as the same in Chimera, right? It is easier for me to use animation in Chimera to make the movie, but I have all my sessions with colored density map in Chimera, I know I could use commands to make such kind of movie in ChimeraX, but I found it difficult for me. Can you give me some suggestions what should I do? I am sorry that if this bothers you.
Have a nice day!
Best, Lu
Hi Lu, As you have found, ChimeraX does not have an Animation graphical interface currently. Animation GUI is listed among the "Missing Features" in the ChimeraX download page. <https://www.rbvi.ucsf.edu/chimerax/download.html> For information about making ChimeraX movies with command scripts, see the following page in the User Guide and links therein (some of the links are to tutorials): <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> Since you already have the colored maps etc. in Chimera, however, you may prefer to continue using the Animation tool in Chimera. Although Chimera has an "export to ChimeraX" option (menu: File... Export Scene or "export" command) it currently only covers atomic structures and representations, and does not include maps. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 27, 2022, at 1:15 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Begin forwarded message:
Hi, Eric,
Since you are here answering my question, I would like to make use of this opportunity to ask you a question about making movie, I want to make a movie with five different density maps from cryo-EM with different ligands binding in two different conformation, there is no animation interface in ChimeraX as the same in Chimera, right? It is easier for me to use animation in Chimera to make the movie, but I have all my sessions with colored density map in Chimera, I know I could use commands to make such kind of movie in ChimeraX, but I found it difficult for me. Can you give me some suggestions what should I do? I am sorry that if this bothers you.
Have a nice day!
Best, Lu
Hi, Elaine, Thank you so much for your reply about my question, I will try the scripts in the User Guide, since I have all the colored maps in ChimeraX (not Chimera), I prefer to use Animation in Chimera because I know how to use it, but in ChimeraX this is one of the missing features, so I want to ask about this question in my previous email, if I couldn't manage to make the movie with maps in ChimeraX ( I prefer to use maps because I have very high resolutions and want to show them), I will make it with atomic structures in Chimera, thank you so much for your kindly explanation. It helps me a lot and I am very happy to receive your email. Wish you a very nice day! Lu Yang Ph.D student Unité de Microbiologie Structurale Institut Pasteur 25, rue du Dr. Roux 75015 <tel:75015> Paris Tel: +33 (0)6 31234426 <tel:+33(0)787329468> +33 (0)1 45688349 -- On 27/06/2022 22:25, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: Hi Lu, As you have found, ChimeraX does not have an Animation graphical interface currently. Animation GUI is listed among the "Missing Features" in the ChimeraX download page. <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/download.html... > For information about making ChimeraX movies with command scripts, see the following page in the User Guide and links therein (some of the links are to tutorials): <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/movies.... > Since you already have the colored maps etc. in Chimera, however, you may prefer to continue using the Animation tool in Chimera. Although Chimera has an "export to ChimeraX" option (menu: File... Export Scene or "export" command) it currently only covers atomic structures and representations, and does not include maps. <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid... > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 27, 2022, at 1:15 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > Begin forwarded message: > > Hi, Eric, > > Since you are here answering my question, I would like to make use of this > opportunity to ask you a question about making movie, I want to make a > movie with five different density maps from cryo-EM with different ligands > binding in two different conformation, there is no animation interface in > ChimeraX as the same in Chimera, right? It is easier for me to use > animation in Chimera to make the movie, but I have all my sessions with > colored density map in Chimera, I know I could use commands to make such > kind of movie in ChimeraX, but I found it difficult for me. Can you give > me some suggestions what should I do? I am sorry that if this bothers you. > > Have a nice day! > > Best, > Lu
Hi Lu, I just wanted to make clear that both Chimera and ChimeraX can make movies with both maps and atomic structures. What I said about "does not include maps" applies only to the Chimera-to-ChimeraX exporting feature. Elaine
On Jun 27, 2022, at 1:45 PM, Lu YANG via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, Elaine,
Thank you so much for your reply about my question, I will try the scripts in the User Guide, since I have all the colored maps in ChimeraX (not Chimera), I prefer to use Animation in Chimera because I know how to use it, but in ChimeraX this is one of the missing features, so I want to ask about this question in my previous email, if I couldn't manage to make the movie with maps in ChimeraX ( I prefer to use maps because I have very high resolutions and want to show them), I will make it with atomic structures in Chimera, thank you so much for your kindly explanation. It helps me a lot and I am very happy to receive your email.
Wish you a very nice day!
Lu Yang Ph.D student Unité de Microbiologie Structurale Institut Pasteur 25, rue du Dr. Roux 75015 <tel:75015> Paris Tel: +33 (0)6 31234426 <tel:+33(0)787329468> +33 (0)1 45688349 --
On 27/06/2022 22:25, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Lu, As you have found, ChimeraX does not have an Animation graphical interface currently. Animation GUI is listed among the "Missing Features" in the ChimeraX download page. <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/download.html... >
For information about making ChimeraX movies with command scripts, see the following page in the User Guide and links therein (some of the links are to tutorials): <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/movies.... >
Since you already have the colored maps etc. in Chimera, however, you may prefer to continue using the Animation tool in Chimera. Although Chimera has an "export to ChimeraX" option (menu: File... Export Scene or "export" command) it currently only covers atomic structures and representations, and does not include maps. <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid... >
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 27, 2022, at 1:15 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Begin forwarded message:
Hi, Eric,
Since you are here answering my question, I would like to make use of this opportunity to ask you a question about making movie, I want to make a movie with five different density maps from cryo-EM with different ligands binding in two different conformation, there is no animation interface in ChimeraX as the same in Chimera, right? It is easier for me to use animation in Chimera to make the movie, but I have all my sessions with colored density map in Chimera, I know I could use commands to make such kind of movie in ChimeraX, but I found it difficult for me. Can you give me some suggestions what should I do? I am sorry that if this bothers you.
Have a nice day!
Best, Lu
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi, Elaine, Thanks for the clarification, I totally understand now, I will try to make it with scripts in ChimeraX. Have a nice day! Best, Lu ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, June 27, 2022 11:04 PM To: Lu YANG <lu.yang@pasteur.fr> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Marking movies in ChimeraX Hi Lu, I just wanted to make clear that both Chimera and ChimeraX can make movies with both maps and atomic structures. What I said about "does not include maps" applies only to the Chimera-to-ChimeraX exporting feature. Elaine
On Jun 27, 2022, at 1:45 PM, Lu YANG via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, Elaine,
Thank you so much for your reply about my question, I will try the scripts in the User Guide, since I have all the colored maps in ChimeraX (not Chimera), I prefer to use Animation in Chimera because I know how to use it, but in ChimeraX this is one of the missing features, so I want to ask about this question in my previous email, if I couldn't manage to make the movie with maps in ChimeraX ( I prefer to use maps because I have very high resolutions and want to show them), I will make it with atomic structures in Chimera, thank you so much for your kindly explanation. It helps me a lot and I am very happy to receive your email.
Wish you a very nice day!
Lu Yang Ph.D student Unité de Microbiologie Structurale Institut Pasteur 25, rue du Dr. Roux 75015 <tel:75015> Paris Tel: +33 (0)6 31234426 <tel:+33(0)787329468> +33 (0)1 45688349 --
On 27/06/2022 22:25, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Lu, As you have found, ChimeraX does not have an Animation graphical interface currently. Animation GUI is listed among the "Missing Features" in the ChimeraX download page. <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/download.html... >
For information about making ChimeraX movies with command scripts, see the following page in the User Guide and links therein (some of the links are to tutorials): <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/movies.... >
Since you already have the colored maps etc. in Chimera, however, you may prefer to continue using the Animation tool in Chimera. Although Chimera has an "export to ChimeraX" option (menu: File... Export Scene or "export" command) it currently only covers atomic structures and representations, and does not include maps. <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid... >
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 27, 2022, at 1:15 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Begin forwarded message:
Hi, Eric,
Since you are here answering my question, I would like to make use of this opportunity to ask you a question about making movie, I want to make a movie with five different density maps from cryo-EM with different ligands binding in two different conformation, there is no animation interface in ChimeraX as the same in Chimera, right? It is easier for me to use animation in Chimera to make the movie, but I have all my sessions with colored density map in Chimera, I know I could use commands to make such kind of movie in ChimeraX, but I found it difficult for me. Can you give me some suggestions what should I do? I am sorry that if this bothers you.
Have a nice day!
Best, Lu
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
Hi Lu, In case this is helpful, you can also find here some example movie scripts I made: https://github.com/Guillawme/chimerax-viz <https://github.com/Guillawme/chimerax-viz> Cheers, Guillaume
On 27 Jun 2022, at 23:12, Lu YANG via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, Elaine,
Thanks for the clarification, I totally understand now, I will try to make it with scripts in ChimeraX.
Have a nice day!
Best, Lu From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, June 27, 2022 11:04 PM To: Lu YANG <lu.yang@pasteur.fr> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Marking movies in ChimeraX
Hi Lu, I just wanted to make clear that both Chimera and ChimeraX can make movies with both maps and atomic structures. What I said about "does not include maps" applies only to the Chimera-to-ChimeraX exporting feature. Elaine
On Jun 27, 2022, at 1:45 PM, Lu YANG via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, Elaine,
Thank you so much for your reply about my question, I will try the scripts in the User Guide, since I have all the colored maps in ChimeraX (not Chimera), I prefer to use Animation in Chimera because I know how to use it, but in ChimeraX this is one of the missing features, so I want to ask about this question in my previous email, if I couldn't manage to make the movie with maps in ChimeraX ( I prefer to use maps because I have very high resolutions and want to show them), I will make it with atomic structures in Chimera, thank you so much for your kindly explanation. It helps me a lot and I am very happy to receive your email.
Wish you a very nice day!
Lu Yang Ph.D student Unité de Microbiologie Structurale Institut Pasteur 25, rue du Dr. Roux 75015 <tel:75015> Paris Tel: +33 (0)6 31234426 <tel:+33(0)787329468> +33 (0)1 45688349 --
On 27/06/2022 22:25, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Lu, As you have found, ChimeraX does not have an Animation graphical interface currently. Animation GUI is listed among the "Missing Features" in the ChimeraX download page. < <applewebdata://B41C3035-7428-46AD-A908-0B0003F2448F>https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/download.html... >
For information about making ChimeraX movies with command scripts, see the following page in the User Guide and links therein (some of the links are to tutorials): < <applewebdata://B41C3035-7428-46AD-A908-0B0003F2448F>https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/movies.... >
Since you already have the colored maps etc. in Chimera, however, you may prefer to continue using the Animation tool in Chimera. Although Chimera has an "export to ChimeraX" option (menu: File... Export Scene or "export" command) it currently only covers atomic structures and representations, and does not include maps. < <applewebdata://B41C3035-7428-46AD-A908-0B0003F2448F>https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid... >
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 27, 2022, at 1:15 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Begin forwarded message:
Hi, Eric,
Since you are here answering my question, I would like to make use of this opportunity to ask you a question about making movie, I want to make a movie with five different density maps from cryo-EM with different ligands binding in two different conformation, there is no animation interface in ChimeraX as the same in Chimera, right? It is easier for me to use animation in Chimera to make the movie, but I have all my sessions with colored density map in Chimera, I know I could use commands to make such kind of movie in ChimeraX, but I found it difficult for me. Can you give me some suggestions what should I do? I am sorry that if this bothers you.
Have a nice day!
Best, Lu
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime... <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Elaine Meng -
Eric Pettersen -
Guillaume Gaullier -
Lu YANG