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I have an assignment for 6th grade biology. I have to look at a 3D structure of a protein and manipulate it so it only shows the AA I’m interested in currently.

what I already did I already looked up the programs most used for this and they point me to JMol and Yasara but the download files are .bin files and the like and I don’t I don’t understand which file is the one I should download and how to install it.

Can someone help me please ?

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Jmol: how to install

Here are instructions for getting Jmol to run on a Mac (or with a slight variation in the runtime file you need to download and the security warnings, on a PC).

  1. Download Jmol from
    https://sourceforge.net/projects/jmol/files/latest/download?source=files
  2. The name of the file will be something like Jmol-14.29.16-binary.zip. Double-click to unzip.
  3. The unzipped folder has a confusing variety of files. This is because most are used for setting up web pages with Jmol embedded. However there is a double-clickable desktop application without any icon and the unpromising name of: Jmol.jar. When you double-click to launch it you will most likely get a message as shown below (1):

Install alerts

To get round this you must either control-click or right-click and select `Open With > Jar Launcher as shown above (2).

Click ‘Open’. (Next time it will just launch without right-clicking.)

  1. Now, in my case the program launches because I have the Java runtime installed on my machines, but you will probably have to download and install this.
  2. Go to the Oracle Java website at http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
    Download and install the appropriate Java SE Runtime Environment, e.g jre-8u172-macosx-x64.dmg

  3. Try launching jmol.jar again. It should work this time.

Jmol: how to use

Because of their emphasis on Jmol in relation to the web, the developers of Jmol do not provide an easy entry to the desktop program. However you can find a clearly illustrated series of web tutorials at the MSOI Centre for Biomoleclar Modelling. I’d highly recommend this as a starting guide.

Although I am not going to describe how you can visualize particular amino acids as that is part of the poster’s project and can be found in the instructions. there are a couple of pointers I would make about things that are not entirely obvious.

  1. After you have loaded a protein from the file menu, you will probably want to change its representation, not least because it may be surrounded by red balls (oxygens from water). To do this you need to right click (or click on the Jmol text on the bottom right) and go through two levels of submenus to select an appropriate representation, as shown.

Selecting a protein display style

  1. In order to make the selections you require you will need to issue commands in the ‘Console’. This can be selected from the File menu:

Jmol Console

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  • $\begingroup$ I've just updated my post with a link to a site with a well illustrated introductory tutorial. I use Jmol/JSmol myself, so I am happy to try to answer questions that member may have. $\endgroup$ – David Jun 15 '18 at 20:34
  • $\begingroup$ I've expanded my instructions for getting started because this is not intuitive. $\endgroup$ – David Jun 16 '18 at 18:41
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You could use an online molecular viewer for this. A fairly complete list is available in Wikipedia as well as in JMol wiki.

In particular, JMol that you tried to install has also a JavaScript version called JSMol that you can use on any website that embeds JSMol: RCSB, Proteopedia, a JSMol tutorial, and many more. To load own structure in JSMol: right click and select File > Load > Open Local File.

If you'd prefer a desktop program, there is also plenty of them: JMol, PyMOL, Chimera, VMD, CCP4mg, etc. All of these are free for non-commercial use (some are even free for commercial use) and work on Mac.

The most popular file format for storing 3D structures of protein is the PDB format. If you would not be able to make your viewer of choice to show only the amino-acids you want, you can always open the PDB file in a text editor and remove lines (atoms) that you don't need.

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LiteMol Viewer, an HTML5 web application for 3D visualization of molecules and other related data.

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Avogadro has a mac version you can use. https://avogadro.cc/

I found it simple.

edit:

You can view the protein you listed here, maybe? ( I am on windows so I do not know if this web app works perfect on mac OS)

https://www.ncbi.nlm.nih.gov/Structure/pdb/1C9O

then in the bottom left corner of the structure image box, there will be a small box icon with arrow.

.

Then you can click on View Sequences and Annotations, under the window tab.

enter image description here

You can then click on the details tab and then left click and drag on the Amino acid sequence to highlight them on the sequence and where they are on the corresponding structure.

enter image description here

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  • $\begingroup$ Crashed when I tried to load 1c9o.pdb on Mavericks. $\endgroup$ – David Jun 16 '18 at 18:47

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