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
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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:
- Re: (no subject) (Thomas Cheatham)
- MD analysis of ion position (Elaine Meng)
- Re: Chimera Visualization Tool (Ela Ka)
- 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 -
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
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:
- Re: (no subject) (Thomas Cheatham)
- MD analysis of ion position (Elaine Meng)
- Re: Chimera Visualization Tool (Ela Ka)
- 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 -
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:
- Re: (no subject) (Thomas Cheatham)
- MD analysis of ion position (Elaine Meng)
- Re: Chimera Visualization Tool (Ela Ka)
- 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