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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)
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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-simulation-of-double-stranded-dna-solvation-and-salt-concerns-article-v1-0
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-simulation-of-double-stranded-dna-solvation-and-salt-concerns-article-v1-0
>
> 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
>
>
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Message: 4
Date: Thu, 25 Feb 2021 13:53:38 +0000
From: David Leeming <david.leeming@student.manchester.ac.uk>
To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>
Subject: [Chimera-users] Chimera help submission
Message-ID:
<LO3P265MB210793AE0AFA7155434571C18C9E9@LO3P265MB2107.GBRP265.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
Dear Chimera users,
I'm attempting to write a chimera script to automate the process of calculating the relative exposure of residues as per this tutorial: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html
The script I have is as follows:
rc('surface') # defines areaSES of residues
rc('defattr C:/Users/Admin/Downloads/areaSESgxg.txt log 0') # define attribute using areaSESgxg.txt
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for r in m.residues:
r.relSESA = r.areaSES/ r.areaSESgxg
However, when I run this script, I am receiving this error:
[cid:39cc50d4-a627-494c-b0f5-411a7785a9a2]
When I run the process using the UI I can successfully calculate relSESA
By using the command: "surface"
Then using the assign attribute function to assign areaSESgxg.txt
Followed by using the calculate attribute function to calculate per residue: residue.areaSES/ residue.areaSESgxg
Could you advise on any methods I could use to fix this script to produce the output I am receiving from the UI.
Kind regards,
David
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