Ask for help with chimeraX
Dear UCSF ChimeraX： We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The SummerX? Hope to get help from your school and restore me, thank you.
Sorry, I do not understand what you want, because there is nothing in Chimera called "Organization"! For ChimeraX, all of the current features are listed in the User Guide: <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html> ...and plugins are available from the ChimeraX Toolshed: <https://cxtoolshed.rbvi.ucsf.edu/> ...and a few additional related software packages are listed here: <https://www.rbvi.ucsf.edu/chimerax/related/index.html> If the feature is not there, as far as we know, it is not available and you would need to keep using Chimera for that feature. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2022, at 6:59 AM, 培慧 张 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF ChimeraX： We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The SummerX? Hope to get help from your school and restore me, thank you.
I'm sorry. What I want to say is the function of animation 发自我的iPhone ------------------ Original ------------------ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Fri,Feb 25,2022 1:05 AM To: 培慧 张 <zph601841656@hotmail.com>, 泡沫 <601841656@qq.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Ask for help with chimeraX Sorry, I do not understand what you want, because there is nothing in Chimera called "Organization"! For ChimeraX, all of the current features are listed in the User Guide: <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>; ...and plugins are available from the ChimeraX Toolshed: <https://cxtoolshed.rbvi.ucsf.edu/>; ...and a few additional related software packages are listed here: <https://www.rbvi.ucsf.edu/chimerax/related/index.html>; If the feature is not there, as far as we know, it is not available and you would need to keep using Chimera for that feature. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 24, 2022, at 6:59 AM, 培慧 张 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Dear UCSF ChimeraX： > We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The SummerX? > Hope to get help from your school and restore me, thank you. >
Hello, We would like to add something like the Animation tool to ChimeraX, but it is a big project and has not yet been done. Even without an Animation tool, you can make movies in ChimeraX now, however: (A) There is an icon on the Home tool bar that looks like a movie camera; clicking that icon will make a simple "spin movie" (rotates the view and automatically saves a movie). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home> (B) Or if you want to make more complicated movies, you would need to use ChimeraX command scripts, as discussed in these recent posts to the list: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003363.html> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003373.html> If you don't want to use anything except the Animation tool, you would have to keep using Chimera for now. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2022, at 7:46 PM, 泡沫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I'm sorry. What I want to say is the function of animation
发自我的iPhone
------------------ Original ------------------ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Fri,Feb 25,2022 1:05 AM To: 培慧 张 <zph601841656@hotmail.com>, 泡沫 <601841656@qq.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Ask for help with chimeraX
Sorry, I do not understand what you want, because there is nothing in Chimera called "Organization"!
For ChimeraX, all of the current features are listed in the User Guide: <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>
...and plugins are available from the ChimeraX Toolshed: <https://cxtoolshed.rbvi.ucsf.edu/>
...and a few additional related software packages are listed here: <https://www.rbvi.ucsf.edu/chimerax/related/index.html>
If the feature is not there, as far as we know, it is not available and you would need to keep using Chimera for that feature.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2022, at 6:59 AM, 培慧 张 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF ChimeraX： We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The SummerX? Hope to get help from your school and restore me, thank you.
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
For larger proteins, what should Chimera do if she makes a mistake in calculating the surface area? 发自我的iPhone ------------------ Original ------------------ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Sat,Feb 26,2022 0:16 AM To: 泡沫 <601841656@qq.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: ChimeraX does not yet have Animation tool Hello, We would like to add something like the Animation tool to ChimeraX, but it is a big project and has not yet been done. Even without an Animation tool, you can make movies in ChimeraX now, however: (A) There is an icon on the Home tool bar that looks like a movie camera; clicking that icon will make a simple "spin movie" (rotates the view and automatically saves a movie). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html>; <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home>; (B) Or if you want to make more complicated movies, you would need to use ChimeraX command scripts, as discussed in these recent posts to the list: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003363.html...; <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003373.html...; If you don't want to use anything except the Animation tool, you would have to keep using Chimera for now. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 24, 2022, at 7:46 PM, 泡沫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > I'm sorry. What I want to say is the function of animation > > 发自我的iPhone > > > ------------------ Original ------------------ > From: Elaine Meng <meng@cgl.ucsf.edu> > Date: Fri,Feb 25,2022 1:05 AM > To: 培慧 张 <zph601841656@hotmail.com>, 泡沫 <601841656@qq.com> > Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> > Subject: Re: [chimerax-users] Ask for help with chimeraX > > Sorry, I do not understand what you want, because there is nothing in Chimera called "Organization"! > > For ChimeraX, all of the current features are listed in the User Guide: > <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>; > > ...and plugins are available from the ChimeraX Toolshed: > <https://cxtoolshed.rbvi.ucsf.edu/>; > > ...and a few additional related software packages are listed here: > <https://www.rbvi.ucsf.edu/chimerax/related/index.html>; > > If the feature is not there, as far as we know, it is not available and you would need to keep using Chimera for that feature. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 24, 2022, at 6:59 AM, 培慧 张 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > > > Dear UCSF ChimeraX： > > We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The SummerX? > > Hope to get help from your school and restore me, thank you. > > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX does not have this surface problem, so you could use ChimeraX. However, if you still need Chimera (because of Animation or some other reason), this page gives some possible workarounds for showing a surface in Chimera: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> I hope this helps, Elaine
On Feb 25, 2022, at 8:47 AM, 泡沫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
For larger proteins, what should Chimera do if she makes a mistake in calculating the surface area?
发自我的iPhone
------------------ Original ------------------ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Sat,Feb 26,2022 0:16 AM To: 泡沫 <601841656@qq.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: ChimeraX does not yet have Animation tool
Hello, We would like to add something like the Animation tool to ChimeraX, but it is a big project and has not yet been done.
Even without an Animation tool, you can make movies in ChimeraX now, however:
(A) There is an icon on the Home tool bar that looks like a movie camera; clicking that icon will make a simple "spin movie" (rotates the view and automatically saves a movie). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home>
(B) Or if you want to make more complicated movies, you would need to use ChimeraX command scripts, as discussed in these recent posts to the list: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003363.html> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003373.html>
If you don't want to use anything except the Animation tool, you would have to keep using Chimera for now.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2022, at 7:46 PM, 泡沫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I'm sorry. What I want to say is the function of animation
发自我的iPhone
------------------ Original ------------------ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Fri,Feb 25,2022 1:05 AM To: 培慧 张 <zph601841656@hotmail.com>, 泡沫 <601841656@qq.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Ask for help with chimeraX
Sorry, I do not understand what you want, because there is nothing in Chimera called "Organization"!
For ChimeraX, all of the current features are listed in the User Guide: <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>
...and plugins are available from the ChimeraX Toolshed: <https://cxtoolshed.rbvi.ucsf.edu/>
...and a few additional related software packages are listed here: <https://www.rbvi.ucsf.edu/chimerax/related/index.html>
If the feature is not there, as far as we know, it is not available and you would need to keep using Chimera for that feature.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2022, at 6:59 AM, 培慧 张 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF ChimeraX： We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The SummerX? Hope to get help from your school and restore me, thank you.
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you very much for your help. I will solve the problem according to your tips. Thank you again 发自我的iPhone ------------------ Original ------------------ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Sat,Feb 26,2022 1:00 AM To: 泡沫 <601841656@qq.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] ChimeraX does not yet have Animation tool ChimeraX does not have this surface problem, so you could use ChimeraX. However, if you still need Chimera (because of Animation or some other reason), this page gives some possible workarounds for showing a surface in Chimera: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>; I hope this helps, Elaine > On Feb 25, 2022, at 8:47 AM, 泡沫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > For larger proteins, what should Chimera do if she makes a mistake in calculating the surface area? > > 发自我的iPhone > > > ------------------ Original ------------------ > From: Elaine Meng <meng@cgl.ucsf.edu> > Date: Sat,Feb 26,2022 0:16 AM > To: 泡沫 <601841656@qq.com> > Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> > Subject: Re: ChimeraX does not yet have Animation tool > > Hello, > We would like to add something like the Animation tool to ChimeraX, but it is a big project and has not yet been done. > > Even without an Animation tool, you can make movies in ChimeraX now, however: > > (A) There is an icon on the Home tool bar that looks like a movie camera; clicking that icon will make a simple "spin movie" (rotates the view and automatically saves a movie). > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html>; > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home>; > > (B) Or if you want to make more complicated movies, you would need to use ChimeraX command scripts, as discussed in these recent posts to the list: > <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003363.html...; > <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003373.html...; > > If you don't want to use anything except the Animation tool, you would have to keep using Chimera for now. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 24, 2022, at 7:46 PM, 泡沫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > > > I'm sorry. What I want to say is the function of animation > > > > 发自我的iPhone > > > > > > ------------------ Original ------------------ > > From: Elaine Meng <meng@cgl.ucsf.edu> > > Date: Fri,Feb 25,2022 1:05 AM > > To: 培慧 张 <zph601841656@hotmail.com>, 泡沫 <601841656@qq.com> > > Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> > > Subject: Re: [chimerax-users] Ask for help with chimeraX > > > > Sorry, I do not understand what you want, because there is nothing in Chimera called "Organization"! > > > > For ChimeraX, all of the current features are listed in the User Guide: > > <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>; > > > > ...and plugins are available from the ChimeraX Toolshed: > > <https://cxtoolshed.rbvi.ucsf.edu/>; > > > > ...and a few additional related software packages are listed here: > > <https://www.rbvi.ucsf.edu/chimerax/related/index.html>; > > > > If the feature is not there, as far as we know, it is not available and you would need to keep using Chimera for that feature. > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 24, 2022, at 6:59 AM, 培慧 张 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > > > > > Dear UCSF ChimeraX： > > > We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The SummerX? > > > Hope to get help from your school and restore me, thank you. > > > > > _______________________________________________ > > ChimeraX-users mailing list > > ChimeraX-users@cgl.ucsf.edu > > Manage subscription: > > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
培慧 张 -
泡沫