[Chimera-users] Chimera-users Digest, Vol 214, Issue 8

Thu Feb 25 21:36:40 PST 2021

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:
>
>> Send Chimera-users mailing list submissions to
>>         chimera-users at 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 at cgl.ucsf.edu
>>
>> You can reach the person managing the list at
>>         chimera-users-owner at 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 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
>> >
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210224/8b5736e0/attachment-0001.html
>> >
>>
>> ------------------------------
>>
>> 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
>> >
>>
>> 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
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210225/d871993c/attachment.html
>> >
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: Outlook-1he3xhiv.png
>> Type: image/png
>> Size: 96706 bytes
>> Desc: Outlook-1he3xhiv.png
>> URL: <
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210225/d871993c/attachment.png
>> >
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> Manage subscription:
>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>> ------------------------------
>>
>> End of Chimera-users Digest, Vol 214, Issue 8
>> *********************************************
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210226/ad4e38c8/attachment.html>