Installing Ribbons on a Macintosh computer running OS X 10


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Installing Ribbons on a Macintosh computer running OS X 10

  1. 1. Macintosh Instructions for Ribbons 10/7/04 Installing Ribbons on a Macintosh computer running OS X (installation tested using OS X 10.3.5) 1. Download and install Apple’s X-windows software, X11 - 2. Download Ribbons and the required Unix files from the University of Alabama Birmingham web site. The Mac OS X executable files for Ribbons and required additional Unix files can be found at You must first get a license from Mike Carson to download and use this software ( Once there, download the following files to a Ribbons folder in your Applications folder. a) rib_macx2.tar.Z – this is the Ribbons application b) Next navigate to the Base Distribution files that are required to run Ribbons and download them to the same Ribbons folder. 1) untar322.csh – needed to unpack the files (Stuffit will unpack the files as well) 2) rib_data.tar.z - Examples and sample data 3) rib_misc.tar.z - Assorted extras 4) rib_elmo.tar.z - Helper Tcl/Tk code 5) rib_bins.tar.z - utility scripts 6) rib_bine.tar.z - Tcl/Tk GUI scripts c) In addition to these files, download the following optional (but recommended) files. 1) rib_html.tar.z - Online manual in HTML format 2) rib_gif1.tar.z - Online manual images GIF format, vol.1 3) rib_gif2.tar.z - Online manual images GIF format, vol.2 4) rib_man1.tar.z - Help in PDF format, with bookmarks 5) rib_img1.tar.z - Artistic/Historic image gallery in *.gif format 6) rib_test.tar.z - Test suite 3. Download Fink from (select the binary installer). This is an excellent utility that will greatly simplify the installation of required Unix libraries, widgets, etc., so that your Unix programs will run. Fink will install as a folder named “sw” in your root directory (“My_Hard_Drive” level). At the end of the installation, Fink will ask if it is OK to install a file called .chrsc in your user directory. Answer yes, as you will want to use this file to set up Ribbons to run. • After running the Fink installer, drag the folder called FinkCommander (see picture below) to the new sw directory and place inside the Fink folder. Next, launch FinkCommander. 1
  2. 2. Macintosh Instructions for Ribbons 10/7/04 Note: Once launched, FinkCommander may tell you that there is a newer version of FinkCommander and direct you to its location for downloading. After down- loading, replace the old version in the sw directory with this new version. After the updated FinkCommander is launched it will connect to an online database of Unix libraries, widgets, etc., and show you a list of all that are available, what their current version is, and more important, whether or not you have it installed. Navigate down the list and install the following: 1) Motif libraries openmotif3, openmotif3-bin, and openmotif3-shlibs 2) TIFF image libraries libtiff, libtiff-bin, and libtiff-shlibs 3) Tcl/Tk scripting languages tcltk, tcltk-dev, and tcltk-shlibs This is an example of the installation of openmotif. Shift-click on all the packages you need and click the install button in the top left corner of the window (as shown below). Some of these packages will ask for confirmation to install, others will simply install directly. Installation may take a few minutes for each one of these packages. The program will let you know when it has finished installing (check the lower part of the window for progress and info). After you have installed all 3 of the above packages, exit FinkCommander. 4. Unpacking Ribbons a) Launch X11 and open a terminal window. If your Ribbons folder is in your Applications folder, type: cd /applications/ribbons 2
  3. 3. Macintosh Instructions for Ribbons 10/7/04 If your Ribbons folder is located elsewhere, such as your user application directory, then modify the command. For example: cd /user/yourusernamehere/applications/ribbons Mac users are not used to this type of directory specification, but if you simply follow the tree structure of your OS X finder window when in column view, it should be easy to figure out. b) Now that your terminal is pointed at your Ribbons directory (folder), unpack the files by typing: csh untar322.csh This command will generate a lot of activity and create a large number of files. It should conclude with no error messages. 5. Finally, you must Set your Environment. NOTE: Before you do this, be aware that all of these instructions are for running only in the tcsh Unix shell. To determine that you are running the tcsh shell, launch X11 and type echo $SHELL at your prompt. If it responds /bin/tcsh then you are using the tcsh shell. If there is no reply or an error message returns, you are probably running a different shell (e. g. bash or zsh). If you are running Mac OS X 10.3.x, it is probably running the bash shell by default. If you do not want to change to tcsh, you will have to figure out the correct syntax for executing these commands for your shell on your own. If you want to make tcsh your default shell when running X11, it is pretty easy to do following these steps. 1. Quit Terminal and X11. 2. Launch Netinfo Manager. It is in your Utilities folder in your Applications folder. 3. Once the window opens, locate users in the second column. Click on users and find your username (the name of your home directory) and click on it. 4. Once you have selected your username, a list of Properties and Values will show in the lower panel of the window. They will likely be “greyed” out, indicating that they can not be edited. To unlock them, click on the lock in the lower left corner of the Netinfo Manager window, enter your password as requested, and you will then be able to edit these Values (they will now be black, not grey). 5. Scroll down the list of Properties and find the one called shell. Next to shell, it will say either /bin/bash or /bin/zsh if you are not running tcsh. If it already says /bin/tcsh, then you can stop here and close Netinfo Manager. 6. Double click on the /bin/bash or /bin/zsh and change it to /bin/tcsh. That is all there is to it. Close the lock by clicking on it, quit Netinfo Manager, and then Log Out of your user account. You must Log Out of your account and then log back in again in order for the change to take effect. You 3
  4. 4. Macintosh Instructions for Ribbons 10/7/04 can test your work by running X11 and trying the echo $SHELL command again (described above). Environment Commands A few environment commands must be given before you can run Ribbons. While you can enter the commands listed below manually in the terminal window, you will have to re-enter them every time you re-start X11. The best way to handle this is to put these commands in your .cshrc startup file that was installed during the Fink installation. To edit the .cshrc file, run X11, and at the prompt type: open –a Textedit .cshrc This will open the .cshrc file in Textedit and it should look something like below (unless you have edited it before). Don’t worry if it has more info than listed below, but somewhere in the file you should be able to identify the following command. source /sw/bin/init.csh Add the following lines AFTER the above command: setenv RIBBONS_HOME "/applications/ribbons/" setenv RIBBONS_HELP "/applications/safari/" set path = ( $path $RIBBONS_HOME/bin ) rehash Note: Do not cut and paste these lines of text. We have seen some weird results coming out of Microsoft Word and pasting into the .cshrc file. Also, instead of Safari, you can specify your favorite web browser to be used for the help files in the second command line, but the browser help support does not appear to work yet for the Macintosh. Hopefully this will be fixed in the future. Save the .cshrc file, quit X11, and you are ready to go. Note: If, by some quirk of nature or other error on your part, you managed to mess up your .cshrc file, you will notice that your tcsh shell will not load when X11 starts up. This will disconnect all of your Unix commands, but fear not, it can be fixed. Your .cshrc file can still be opened and repaired using the following command: /usr/bin/open –a Textedit .cshrc Fix the type errors, re-save, and all should work accordingly. 4
  5. 5. Macintosh Instructions for Ribbons 10/7/04 6) See if it works. Restart X11 and issue the following commands: A) Run the interactive demo: ribbons-demo -n his A window should open after initialization, with a small ball & stick model. B) Run with your data: Ribbons requires PDB (Protein Data Bank) files for input. Ribbons works by making a database of lots of little ascii files for display. It requires each macromolecular chain for a ribbon drawing to be in a separate file for best results. Lots of utilities exist to massage the data, and these may be driven by the GUI interface 'ribbons-data'. For illustrations of your favorite molecule, mol.pdb, suggest your create a new directory, go there, copy (or link) your coordinates, then form X11 issue the command: ribbons-data mol Realize that there is a learning curve involved in becoming competent with Ribbons in displaying your crystallographic data, and this learning curve is independent of the computer or operating system you are using. This software does however produce striking, publication quality figures of your structural data. 7) Make it automatic! Finally, instead of typing Ribbons-data in the terminal window each time to run the Ribbons program, you can actually add it to your dock and auto-run it from there. a) Open the Ribbons folder, then the bin folder and locate the Ribbons-data file. b) Drag it to the dock to add it (since it is not an application it has to be added to portion of the dock next to the divider line by the trash can). c) Click on it. The first time you do this, your computer will tell you “There is no default application specified to open this file…..”. Click on “Choose Application…” and locate X11 and select it. From now on, when you click on Ribbons-data, X11 will launch and load the Ribbons-data module. Simplicity, the way it should be. 5