<div dir="auto">My username and password incorrect plese help me </div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 25, 2021, 7:11 PM <<a href="mailto:chimera-users-request@cgl.ucsf.edu">chimera-users-request@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Chimera-users mailing list submissions to<br>
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Today's Topics:<br>
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1. Re: (no subject) (Thomas Cheatham)<br>
2. MD analysis of ion position (Elaine Meng)<br>
3. Re: Chimera Visualization Tool (Ela Ka)<br>
4. Chimera help submission (David Leeming)<br>
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Message: 1<br>
Date: Wed, 24 Feb 2021 21:06:55 +0000<br>
From: Thomas Cheatham <<a href="mailto:tec3@utah.edu" target="_blank" rel="noreferrer">tec3@utah.edu</a>><br>
To: K Jan <<a href="mailto:10dunajkr@gmail.com" target="_blank" rel="noreferrer">10dunajkr@gmail.com</a>>, "<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users@cgl.ucsf.edu</a>"<br>
<<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users@cgl.ucsf.edu</a>><br>
Subject: Re: [Chimera-users] (no subject)<br>
Message-ID: <<a href="mailto:6bbb12c3268847adbbf93577d9f4313a@utah.edu" target="_blank" rel="noreferrer">6bbb12c3268847adbbf93577d9f4313a@utah.edu</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
<br>
The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...<br>
<br>
See: <a href="https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-simulation-of-double-stranded-dna-solvation-and-salt-concerns-article-v1-0" rel="noreferrer noreferrer" target="_blank">https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-simulation-of-double-stranded-dna-solvation-and-salt-concerns-article-v1-0</a><br>
<br>
CPPTRAJ is available in AmberTools or via GitHub - <a href="https://github.com/Amber-MD/" rel="noreferrer noreferrer" target="_blank">https://github.com/Amber-MD/</a><br>
<br>
Also AmberHub may have a tutorial related - <a href="https://amberhub.chpc.utah.edu/making-a-3d-histogram/" rel="noreferrer noreferrer" target="_blank">https://amberhub.chpc.utah.edu/making-a-3d-histogram/</a><br>
<br>
--tec3<br>
<br>
________________________________________<br>
From: Chimera-users <<a href="mailto:chimera-users-bounces@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users-bounces@cgl.ucsf.edu</a>> on behalf of K Jan <<a href="mailto:10dunajkr@gmail.com" target="_blank" rel="noreferrer">10dunajkr@gmail.com</a>><br>
Sent: Wednesday, February 24, 2021 1:53:36 PM<br>
To: <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users@cgl.ucsf.edu</a><br>
Subject: [Chimera-users] (no subject)<br>
<br>
Hello,<br>
<br>
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.<br>
<br>
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.?<br>
<br>
Thanks<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 24 Feb 2021 13:22:02 -0800<br>
From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" rel="noreferrer">meng@cgl.ucsf.edu</a>><br>
To: K Jan <<a href="mailto:10dunajkr@gmail.com" target="_blank" rel="noreferrer">10dunajkr@gmail.com</a>><br>
Cc: "<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users@cgl.ucsf.edu</a>" <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users@cgl.ucsf.edu</a>><br>
Subject: [Chimera-users] MD analysis of ion position<br>
Message-ID: <<a href="mailto:870D7C13-E4ED-49DB-8AA0-5E503A94DCA9@cgl.ucsf.edu" target="_blank" rel="noreferrer">870D7C13-E4ED-49DB-8AA0-5E503A94DCA9@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Thanks, I agree that CPPTRAJ is a great solution for analyzing trajectories. Looks like it can read several formats:<br>
<<a href="https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/" rel="noreferrer noreferrer" target="_blank">https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/</a>><br>
<br>
Alternatively:<br>
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.<br>
<br>
MD Movie help, click "Occupancy Analysis" in the left hand links:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html" rel="noreferrer noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html</a>><br>
<br>
Occupancy analysis is also covered in the last section of this Chimera tutorial:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part2" rel="noreferrer noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part2</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Feb 24, 2021, at 1:06 PM, Thomas Cheatham <<a href="mailto:tec3@utah.edu" target="_blank" rel="noreferrer">tec3@utah.edu</a>> wrote:<br>
> <br>
> <br>
> The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...<br>
> <br>
> See: <a href="https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-simulation-of-double-stranded-dna-solvation-and-salt-concerns-article-v1-0" rel="noreferrer noreferrer" target="_blank">https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-simulation-of-double-stranded-dna-solvation-and-salt-concerns-article-v1-0</a><br>
> <br>
> CPPTRAJ is available in AmberTools or via GitHub - <a href="https://github.com/Amber-MD/" rel="noreferrer noreferrer" target="_blank">https://github.com/Amber-MD/</a><br>
> <br>
> Also AmberHub may have a tutorial related - <a href="https://amberhub.chpc.utah.edu/making-a-3d-histogram/" rel="noreferrer noreferrer" target="_blank">https://amberhub.chpc.utah.edu/making-a-3d-histogram/</a><br>
> <br>
> --tec3<br>
> <br>
> ________________________________________<br>
> From: Chimera-users <<a href="mailto:chimera-users-bounces@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users-bounces@cgl.ucsf.edu</a>> on behalf of K Jan <<a href="mailto:10dunajkr@gmail.com" target="_blank" rel="noreferrer">10dunajkr@gmail.com</a>><br>
> Sent: Wednesday, February 24, 2021 1:53:36 PM<br>
> To: <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users@cgl.ucsf.edu</a><br>
> Subject: [Chimera-users] (no subject)<br>
> <br>
> Hello,<br>
> <br>
> 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.<br>
> <br>
> 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.?<br>
> <br>
> Thanks<br>
> <br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 24 Feb 2021 22:18:45 +0330<br>
From: Ela Ka <<a href="mailto:e.kashani.a@gmail.com" target="_blank" rel="noreferrer">e.kashani.a@gmail.com</a>><br>
To: Chimera User Help <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users@cgl.ucsf.edu</a>><br>
Subject: Re: [Chimera-users] Chimera Visualization Tool<br>
Message-ID:<br>
<<a href="mailto:CAFiNxG3Ca3WthCUCR3Oad2bt%2Bi6mmMSTsCAkOTvG3oez7s1dzQ@mail.gmail.com" target="_blank" rel="noreferrer">CAFiNxG3Ca3WthCUCR3Oad2bt+i6mmMSTsCAkOTvG3oez7s1dzQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Elaine,<br>
<br>
Thank you very much. I appreciate your consideration. Sure, we'll take care<br>
of the credit and other considerations.<br>
<br>
Best Regards<br>
Elaheh Kashani-Amin<br>
<br>
On Wed, Feb 24, 2021, 10:13 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" rel="noreferrer">meng@cgl.ucsf.edu</a>> wrote:<br>
<br>
> Dear Elaheh Kashani-Amin,<br>
> Thanks for asking. Yes, it would be acceptable to use Chimera (free<br>
> version) to create images for your slides, providing that Chimera is<br>
> credited for the images in these materials.<br>
><br>
> However, if you were going to use Chimera interactively as part of the<br>
> paid educational sessions, your group would need to license the software as<br>
> described here:<br>
> <<a href="https://www.rbvi.ucsf.edu/chimera/commercial_license.html" rel="noreferrer noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/commercial_license.html</a>><br>
><br>
> Best regards,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
><br>
> > On Feb 24, 2021, at 2:40 AM, Ela Ka <<a href="mailto:e.kashani.a@gmail.com" target="_blank" rel="noreferrer">e.kashani.a@gmail.com</a>> wrote:<br>
> ><br>
> > Dear Madam/Sir,<br>
> ><br>
> > We are a group of researchers who try to prepare educational contents in<br>
> different aspects of protein molecular modeling for the students. Access to<br>
> these educational content is not free. We need to prepare some pictures of<br>
> proteins, ligand-receptor interaction, etc. for the slides. Can we use the<br>
> Chimera software (free version) to prepare some pictures for the slides?<br>
> Though, we won't use the tool, itself, for those educational sessions.<br>
> ><br>
> > Thank you for your consideration<br>
> ><br>
> > Best Regards<br>
> > Elaheh Kashani-Amin<br>
> > PhD, Bioscience<br>
><br>
><br>
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Message: 4<br>
Date: Thu, 25 Feb 2021 13:53:38 +0000<br>
From: David Leeming <<a href="mailto:david.leeming@student.manchester.ac.uk" target="_blank" rel="noreferrer">david.leeming@student.manchester.ac.uk</a>><br>
To: "<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" rel="noreferrer">chimera-users@cgl.ucsf.edu</a>><br>
Subject: [Chimera-users] Chimera help submission<br>
Message-ID:<br>
<<a href="mailto:LO3P265MB210793AE0AFA7155434571C18C9E9@LO3P265MB2107.GBRP265.PROD.OUTLOOK.COM" target="_blank" rel="noreferrer">LO3P265MB210793AE0AFA7155434571C18C9E9@LO3P265MB2107.GBRP265.PROD.OUTLOOK.COM</a>><br>
<br>
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<br>
Dear Chimera users,<br>
I'm attempting to write a chimera script to automate the process of calculating the relative exposure of residues as per this tutorial: <a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html" rel="noreferrer noreferrer" target="_blank">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html</a><br>
<br>
The script I have is as follows:<br>
rc('surface') # defines areaSES of residues<br>
rc('defattr C:/Users/Admin/Downloads/areaSESgxg.txt log 0') # define attribute using areaSESgxg.txt<br>
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):<br>
for r in m.residues:<br>
r.relSESA = r.areaSES/ r.areaSESgxg<br>
<br>
However, when I run this script, I am receiving this error:<br>
[cid:39cc50d4-a627-494c-b0f5-411a7785a9a2]<br>
When I run the process using the UI I can successfully calculate relSESA<br>
By using the command: "surface"<br>
Then using the assign attribute function to assign areaSESgxg.txt<br>
Followed by using the calculate attribute function to calculate per residue: residue.areaSES/ residue.areaSESgxg<br>
<br>
Could you advise on any methods I could use to fix this script to produce the output I am receiving from the UI.<br>
<br>
Kind regards,<br>
David<br>
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</blockquote></div>