Re: [Chimera-users] Chimera-users Digest, Vol 214, Issue 8
My username and password incorrect plese help me On Thu, Feb 25, 2021, 7:11 PM <chimera-users-request@cgl.ucsf.edu> wrote:
Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu
To subscribe or unsubscribe via the World Wide Web, visit https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu
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When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."
Today's Topics:
1. Re: (no subject) (Thomas Cheatham) 2. MD analysis of ion position (Elaine Meng) 3. Re: Chimera Visualization Tool (Ela Ka) 4. Chimera help submission (David Leeming)
----------------------------------------------------------------------
Message: 1 Date: Wed, 24 Feb 2021 21:06:55 +0000 From: Thomas Cheatham <tec3@utah.edu> To: K Jan <10dunajkr@gmail.com>, "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] (no subject) Message-ID: <6bbb12c3268847adbbf93577d9f4313a@utah.edu> Content-Type: text/plain; charset="us-ascii"
The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...
See: https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-si...
CPPTRAJ is available in AmberTools or via GitHub - https://github.com/Amber-MD/
Also AmberHub may have a tutorial related - https://amberhub.chpc.utah.edu/making-a-3d-histogram/
--tec3
________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of K Jan <10dunajkr@gmail.com> Sent: Wednesday, February 24, 2021 1:53:36 PM To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] (no subject)
Hello,
I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation.
I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.?
Thanks
------------------------------
Message: 2 Date: Wed, 24 Feb 2021 13:22:02 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> To: K Jan <10dunajkr@gmail.com> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] MD analysis of ion position Message-ID: <870D7C13-E4ED-49DB-8AA0-5E503A94DCA9@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii
Thanks, I agree that CPPTRAJ is a great solution for analyzing trajectories. Looks like it can read several formats: <https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/>
Alternatively: In Chimera, if you can view your trajectory in the MD Movie tool, you can also use that tool to calculate and display an occupancy map. I think that's essentially the same thing that Tom mentioned, a density map on a grid that can be viewed as isosurfaces.
MD Movie help, click "Occupancy Analysis" in the left hand links: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie....
Occupancy analysis is also covered in the last section of this Chimera tutorial: < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.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 Feb 24, 2021, at 1:06 PM, Thomas Cheatham <tec3@utah.edu> wrote:
The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...
See: https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-si...
CPPTRAJ is available in AmberTools or via GitHub - https://github.com/Amber-MD/
Also AmberHub may have a tutorial related - https://amberhub.chpc.utah.edu/making-a-3d-histogram/
--tec3
________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of K Jan <10dunajkr@gmail.com> Sent: Wednesday, February 24, 2021 1:53:36 PM To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] (no subject)
Hello,
I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation.
I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.?
Thanks
------------------------------
Message: 3 Date: Wed, 24 Feb 2021 22:18:45 +0330 From: Ela Ka <e.kashani.a@gmail.com> To: Chimera User Help <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera Visualization Tool Message-ID: < CAFiNxG3Ca3WthCUCR3Oad2bt+i6mmMSTsCAkOTvG3oez7s1dzQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
Dear Elaine,
Thank you very much. I appreciate your consideration. Sure, we'll take care of the credit and other considerations.
Best Regards Elaheh Kashani-Amin
On Wed, Feb 24, 2021, 10:13 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Elaheh Kashani-Amin, Thanks for asking. Yes, it would be acceptable to use Chimera (free version) to create images for your slides, providing that Chimera is credited for the images in these materials.
However, if you were going to use Chimera interactively as part of the paid educational sessions, your group would need to license the software as described here: <https://www.rbvi.ucsf.edu/chimera/commercial_license.html>
Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2021, at 2:40 AM, Ela Ka <e.kashani.a@gmail.com> wrote:
Dear Madam/Sir,
We are a group of researchers who try to prepare educational contents in different aspects of protein molecular modeling for the students. Access to these educational content is not free. We need to prepare some pictures of proteins, ligand-receptor interaction, etc. for the slides. Can we use the Chimera software (free version) to prepare some pictures for the slides? Though, we won't use the tool, itself, for those educational sessions.
Thank you for your consideration
Best Regards Elaheh Kashani-Amin PhD, Bioscience
Raheel112 On Fri, Feb 26, 2021, 10:35 AM Khurram Shahzad <ks9699904@gmail.com> wrote:
My username and password incorrect plese help me
On Thu, Feb 25, 2021, 7:11 PM <chimera-users-request@cgl.ucsf.edu> wrote:
Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu
To subscribe or unsubscribe via the World Wide Web, visit https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu
You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."
Today's Topics:
1. Re: (no subject) (Thomas Cheatham) 2. MD analysis of ion position (Elaine Meng) 3. Re: Chimera Visualization Tool (Ela Ka) 4. Chimera help submission (David Leeming)
----------------------------------------------------------------------
Message: 1 Date: Wed, 24 Feb 2021 21:06:55 +0000 From: Thomas Cheatham <tec3@utah.edu> To: K Jan <10dunajkr@gmail.com>, "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] (no subject) Message-ID: <6bbb12c3268847adbbf93577d9f4313a@utah.edu> Content-Type: text/plain; charset="us-ascii"
The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...
See: https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-si...
CPPTRAJ is available in AmberTools or via GitHub - https://github.com/Amber-MD/
Also AmberHub may have a tutorial related - https://amberhub.chpc.utah.edu/making-a-3d-histogram/
--tec3
________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of K Jan <10dunajkr@gmail.com> Sent: Wednesday, February 24, 2021 1:53:36 PM To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] (no subject)
Hello,
I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation.
I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.?
Thanks
------------------------------
Message: 2 Date: Wed, 24 Feb 2021 13:22:02 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> To: K Jan <10dunajkr@gmail.com> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] MD analysis of ion position Message-ID: <870D7C13-E4ED-49DB-8AA0-5E503A94DCA9@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii
Thanks, I agree that CPPTRAJ is a great solution for analyzing trajectories. Looks like it can read several formats: <https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/>
Alternatively: In Chimera, if you can view your trajectory in the MD Movie tool, you can also use that tool to calculate and display an occupancy map. I think that's essentially the same thing that Tom mentioned, a density map on a grid that can be viewed as isosurfaces.
MD Movie help, click "Occupancy Analysis" in the left hand links: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie....
Occupancy analysis is also covered in the last section of this Chimera tutorial: < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.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 Feb 24, 2021, at 1:06 PM, Thomas Cheatham <tec3@utah.edu> wrote:
The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...
See: https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-si...
CPPTRAJ is available in AmberTools or via GitHub - https://github.com/Amber-MD/
Also AmberHub may have a tutorial related - https://amberhub.chpc.utah.edu/making-a-3d-histogram/
--tec3
________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of K Jan <10dunajkr@gmail.com> Sent: Wednesday, February 24, 2021 1:53:36 PM To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] (no subject)
Hello,
I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation.
I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.?
Thanks
------------------------------
Message: 3 Date: Wed, 24 Feb 2021 22:18:45 +0330 From: Ela Ka <e.kashani.a@gmail.com> To: Chimera User Help <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera Visualization Tool Message-ID: < CAFiNxG3Ca3WthCUCR3Oad2bt+i6mmMSTsCAkOTvG3oez7s1dzQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
Dear Elaine,
Thank you very much. I appreciate your consideration. Sure, we'll take care of the credit and other considerations.
Best Regards Elaheh Kashani-Amin
On Wed, Feb 24, 2021, 10:13 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Elaheh Kashani-Amin, Thanks for asking. Yes, it would be acceptable to use Chimera (free version) to create images for your slides, providing that Chimera is credited for the images in these materials.
However, if you were going to use Chimera interactively as part of the paid educational sessions, your group would need to license the software as described here: <https://www.rbvi.ucsf.edu/chimera/commercial_license.html>
Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2021, at 2:40 AM, Ela Ka <e.kashani.a@gmail.com> wrote:
Dear Madam/Sir,
We are a group of researchers who try to prepare educational contents in different aspects of protein molecular modeling for the students. Access to these educational content is not free. We need to prepare some pictures of proteins, ligand-receptor interaction, etc. for the slides. Can we use the Chimera software (free version) to prepare some pictures for the slides? Though, we won't use the tool, itself, for those educational sessions.
Thank you for your consideration
Best Regards Elaheh Kashani-Amin PhD, Bioscience
I do not know your password. Near the bottom of the mailing list management page you can enter your e-mail address (the same one that you signed up with) to "get a password reminder."
I hope this helps, Elaine
On Feb 25, 2021, at 9:36 PM, Khurram Shahzad <ks9699904@gmail.com> wrote:
Raheel112
On Fri, Feb 26, 2021, 10:35 AM Khurram Shahzad <ks9699904@gmail.com> wrote: My username and password incorrect plese help me
On Thu, Feb 25, 2021, 7:11 PM <chimera-users-request@cgl.ucsf.edu> wrote: Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu
To subscribe or unsubscribe via the World Wide Web, visit https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu
You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."
Today's Topics:
1. Re: (no subject) (Thomas Cheatham) 2. MD analysis of ion position (Elaine Meng) 3. Re: Chimera Visualization Tool (Ela Ka) 4. Chimera help submission (David Leeming)
----------------------------------------------------------------------
Message: 1 Date: Wed, 24 Feb 2021 21:06:55 +0000 From: Thomas Cheatham <tec3@utah.edu> To: K Jan <10dunajkr@gmail.com>, "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] (no subject) Message-ID: <6bbb12c3268847adbbf93577d9f4313a@utah.edu> Content-Type: text/plain; charset="us-ascii"
The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...
See: https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-si...
CPPTRAJ is available in AmberTools or via GitHub - https://github.com/Amber-MD/
Also AmberHub may have a tutorial related - https://amberhub.chpc.utah.edu/making-a-3d-histogram/
--tec3
________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of K Jan <10dunajkr@gmail.com> Sent: Wednesday, February 24, 2021 1:53:36 PM To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] (no subject)
Hello,
I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation.
I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.?
Thanks
------------------------------
Message: 2 Date: Wed, 24 Feb 2021 13:22:02 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> To: K Jan <10dunajkr@gmail.com> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] MD analysis of ion position Message-ID: <870D7C13-E4ED-49DB-8AA0-5E503A94DCA9@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii
Thanks, I agree that CPPTRAJ is a great solution for analyzing trajectories. Looks like it can read several formats: <https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/>
Alternatively: In Chimera, if you can view your trajectory in the MD Movie tool, you can also use that tool to calculate and display an occupancy map. I think that's essentially the same thing that Tom mentioned, a density map on a grid that can be viewed as isosurfaces.
MD Movie help, click "Occupancy Analysis" in the left hand links: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
Occupancy analysis is also covered in the last section of this Chimera tutorial: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part2>
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, 2021, at 1:06 PM, Thomas Cheatham <tec3@utah.edu> wrote:
The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...
See: https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-si...
CPPTRAJ is available in AmberTools or via GitHub - https://github.com/Amber-MD/
Also AmberHub may have a tutorial related - https://amberhub.chpc.utah.edu/making-a-3d-histogram/
--tec3
________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of K Jan <10dunajkr@gmail.com> Sent: Wednesday, February 24, 2021 1:53:36 PM To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] (no subject)
Hello,
I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation.
I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.?
Thanks
------------------------------
Message: 3 Date: Wed, 24 Feb 2021 22:18:45 +0330 From: Ela Ka <e.kashani.a@gmail.com> To: Chimera User Help <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera Visualization Tool Message-ID: <CAFiNxG3Ca3WthCUCR3Oad2bt+i6mmMSTsCAkOTvG3oez7s1dzQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
Dear Elaine,
Thank you very much. I appreciate your consideration. Sure, we'll take care of the credit and other considerations.
Best Regards Elaheh Kashani-Amin
On Wed, Feb 24, 2021, 10:13 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Elaheh Kashani-Amin, Thanks for asking. Yes, it would be acceptable to use Chimera (free version) to create images for your slides, providing that Chimera is credited for the images in these materials.
However, if you were going to use Chimera interactively as part of the paid educational sessions, your group would need to license the software as described here: <https://www.rbvi.ucsf.edu/chimera/commercial_license.html>
Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2021, at 2:40 AM, Ela Ka <e.kashani.a@gmail.com> wrote:
Dear Madam/Sir,
We are a group of researchers who try to prepare educational contents in different aspects of protein molecular modeling for the students. Access to these educational content is not free. We need to prepare some pictures of proteins, ligand-receptor interaction, etc. for the slides. Can we use the Chimera software (free version) to prepare some pictures for the slides? Though, we won't use the tool, itself, for those educational sessions.
Thank you for your consideration
Best Regards Elaheh Kashani-Amin PhD, Bioscience
participants (2)
-
Elaine Meng -
Khurram Shahzad