[Chimera-users] Chimera-users Digest, Vol 214, Issue 8
Elaine Meng
meng at cgl.ucsf.edu
Fri Feb 26 08:30:47 PST 2021
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."
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I hope this helps,
Elaine
> On Feb 25, 2021, at 9:36 PM, Khurram Shahzad <ks9699904 at gmail.com> wrote:
>
> Raheel112
>
> On Fri, Feb 26, 2021, 10:35 AM Khurram Shahzad <ks9699904 at gmail.com> wrote:
> My username and password incorrect plese help me
>
> On Thu, Feb 25, 2021, 7:11 PM <chimera-users-request at cgl.ucsf.edu> wrote:
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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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 24 Feb 2021 21:06:55 +0000
> From: Thomas Cheatham <tec3 at utah.edu>
> To: K Jan <10dunajkr at gmail.com>, "chimera-users at cgl.ucsf.edu"
> <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] (no subject)
> Message-ID: <6bbb12c3268847adbbf93577d9f4313a at 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 at cgl.ucsf.edu> on behalf of K Jan <10dunajkr at gmail.com>
> Sent: Wednesday, February 24, 2021 1:53:36 PM
> To: chimera-users at 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 at cgl.ucsf.edu>
> To: K Jan <10dunajkr at gmail.com>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] MD analysis of ion position
> Message-ID: <870D7C13-E4ED-49DB-8AA0-5E503A94DCA9 at 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 at 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 at cgl.ucsf.edu> on behalf of K Jan <10dunajkr at gmail.com>
> > Sent: Wednesday, February 24, 2021 1:53:36 PM
> > To: chimera-users at 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 at gmail.com>
> To: Chimera User Help <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Chimera Visualization Tool
> Message-ID:
> <CAFiNxG3Ca3WthCUCR3Oad2bt+i6mmMSTsCAkOTvG3oez7s1dzQ at 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 at 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 at 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 at student.manchester.ac.uk>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] Chimera help submission
> Message-ID:
> <LO3P265MB210793AE0AFA7155434571C18C9E9 at LO3P265MB2107.GBRP265.PROD.OUTLOOK.COM>
>
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>
> 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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