[Chimera-users] ubuntu 14.04 problem - further information

Boaz Shaanan bshaanan at bgu.ac.il
Mon Sep 18 14:23:20 PDT 2017


Hi,

I picked up from the list of old versions this version from November 2016 chimera-1.11.2-linux_x86_64.bin and it works fine. My recollection is also that last version I worked with, the nightly build from June 2017 also worked fine.
I thought you might be interested in this piece of information.

             Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





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Subject: Chimera-users Digest, Vol 173, Issue 14

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Today's Topics:

   1. Re: COX inhibitor demo discrepancy (Elaine Meng)
   2. morph & ligands (Hernando J Sosa)
   3. ubuntu 14.04 - issue with latest chimera 64 bit (both
      production and recent nightlly build) (Boaz Shaanan)
   4. Do you recieve image submissions? (Frank Irby)
   5. Re: morph & ligands (Hernando J Sosa)


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Message: 1
Date: Sun, 17 Sep 2017 09:54:37 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: simon chapman <rowanlodge19 at gmail.com>
Cc: "chimera-users at cgl.ucsf.edu List" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] COX inhibitor demo discrepancy
Message-ID: <375AFBD6-1B2D-4C2A-8677-B1F7E210D9C9 at cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8

Hi Simon,
(1) There are lots of molecular dynamics programs: AMBER, GROMACS, NAMD etc., and the list of input formats for the Chimera ?MD Movie? tool shows which of those programs? results it can handle:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

Chimera itself even has a Molecular Dynamics SImulation tool (see Tools? MD/Ensemble Analysis) but it is relatively slow. Be aware that there is a learning curve to running MD simulations.  Garbage in gives garbage out, so you have to take some time to learn about the technique and its limitations.  There are many input options and parameters, and just taking all the defaults isn?t usually the path to success for any given molecular system.  There are textbooks on the subject and running a decent simulation could be a project in itself.

Or if you just wanted a conformational ensemble rather than a trajectory, there are a whole host of other programs that do some normal mode analysis based on network models.  Those seem simpler than MD to use, but the results are more limited; that?s just a general impression? I?m not an expert on the topic.

Even simpler is if you have two different conformations of some protein, you can morph between them in Chimera and show the results in Chimera.  For example, see the ?superpositions and alignments? tutorial starting at ?different conformations of the same protein"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html>

(2) References to the papers about the data are given in the MD Movie tutorial.  Part 1 uses MD results (probably from AMBER but you?d have to read the paper to doublecheck) and part 2 uses an NMR ensemble.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>

(3) the browser is showing the text of 1plx.pdb ? you just need to save it as plain text, just like you did for ras.mol2 .  Alternatively, you can get the same file from RCSB PDB, Download Files -> PDB Format:
<http://www.rcsb.org/pdb/explore/explore.do?structureId=1plx>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 16, 2017, at 2:04 PM, simon chapman <rowanlodge19 at gmail.com> wrote:
>
> Thank you Elaine...that did it! Couldn't save as Plaintext, but it still worked as Notepad.
>
> I am very pleased with the MD Movie tutorial...it worked for me without too many changes, and is suitably impressive. Did the authors supplying the data derive them from AMBER?  How can I supply data relevant to the molecules I'm studying to produce the appropriate MD Movie?
>
> Also, and I hope it's OK to bother you again, the attached screenshots show the result of trying to download 1plx.pdb. I've tried several formats, but the message "no pdb structures found" appears every time.  Clicking " 1plx.pdb" in the tutorial leads to the page shown. Selecting "save as..."  leads to  the other two pop-ups in screenshot 1. Downloads lists the file as Tutorial FrameSet, and contains the four files shown in screenshot 2. Feel like I'm going round in circles with this one.
>
> Thanks in advance...despite the challenges, Chimera is very impressive, and should enhance my MSc thesis which commences next month
>
> Best wishes   Simon
>



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Message: 2
Date: Mon, 18 Sep 2017 00:00:22 +0000
From: Hernando J Sosa <hernando.sosa at einstein.yu.edu>
To: chimera List <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] morph & ligands
Message-ID:
        <F0E461AAE34D0448B6EE7D31E433B70801236B9246 at AEWEXCPM21.yuad.uds.yu.edu>

Content-Type: text/plain; charset="utf-8"

 Is there a way to  keep & show the ligands in the Morph between structures?.  In the morphs that I've tried the ligands do not show up.

Thanks

H.




------------------------------

Message: 3
Date: Mon, 18 Sep 2017 14:51:15 +0000
From: Boaz Shaanan <bshaanan at bgu.ac.il>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] ubuntu 14.04 - issue with latest chimera 64
        bit (both production and recent nightlly build)
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        <4B2A491F685D1E4FBBF985E193095AAF012F4BC7A7 at hawk3.auth.ad.bgu.ac.il>
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Message: 4
Date: Sun, 17 Sep 2017 15:39:00 +0000 (UTC)
From: Frank Irby <fourpaws3 at yahoo.com>
To: <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] Do you recieve image submissions?
Message-ID: <295279869.3724177.1505662740916 at mail.yahoo.com>
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https://mandelscape.deviantart.com/art/Luciferase-firefly-703808245

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Message: 5
Date: Mon, 18 Sep 2017 15:30:28 +0000
From: Hernando J Sosa <hernando.sosa at einstein.yu.edu>
To: chimera List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] morph & ligands
Message-ID:
        <F0E461AAE34D0448B6EE7D31E433B70801236B989E at AEWEXCPM21.yuad.uds.yu.edu>

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Sorry that was an old question and here was the answer.

----------------------------------------------------------
As I had understood it (and had written in the documentation)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#pairing>:

"HET residues such as ligands and ions are only included if they are present in both structures and attached to the same atom(s) in the paired chains by at least one "covalent" bond (which can be an unrealistic bond added manually, e.g., with the command bond, and subsequently undisplayed) or ion coordination pseudobond.

Once residues are paired, atoms in common within those residues are paired. In paired residues of the same type, atom pairing is straightforward. In paired residues of different types, only atoms with the same names are paired, and only a single connected fragment is kept per residue."

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


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Sent: Sunday, September 17, 2017 8:00 PM
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Subject: [Chimera-users] morph & ligands

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 Is there a way to  keep & show the ligands in the Morph between structures?.  In the morphs that I've tried the ligands do not show up.

Thanks

H.


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