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Heptmeric SmAP protein from Pyrobaculum aerophilum, courtesy of Cam Mura. Cyan colored surface represents molecular envelope. |
The Ribbons software
interactively displays molecular models, analyzes crystallographic results,
and creates publication quality images. The `ribbon drawing' is featured.
Space-filling, ball-and-stick representations, dot and triangular surfaces,
density map contours, and text are also supported. Coordinate files
must be in Protein Data Bank (*.pdb) format. Auxiliary
programs extract data from the pdb file and make many new files which
are used by the interactive Ribbons interface. It is recommended that you
make a new directory to begin.
Requirements:
Manual for Ribbons:Online or PDF version Ribbons Website:
Further Examples of images from Ribbons:
Reference for Ribbons:
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| You need to source
/joule2/programs/login to get started.
STEP ONE Type: ribbons -e 1I8F.pdb After a couple of seconds, an interactive X-window graphical interface will appear as shown on the right. You will also find that your directory now contains several new files. Ribbons has automatically split the pdb file into seven separate pdb files, each containing one monomer chain of the heptamer: 1I8F_A_pro1.pdb 1I8F_B_pro2.pdb 1I8F_C_pro3.pdb
Secondary structure assignments are written to the following files: 1I8F_A_pro1.ss 1I8F_D_pro4.ss 1I8F_G_pro7.ss 1I8F_B_pro2.ss 1I8F_E_pro5.ss 1I8F_C_pro3.ss 1I8F_F_pro6.ss Heteroatoms (except water) will be extracted and output as balls (*.sph) and sticks (*.cyl) : 1I8F_het1.pdb coordinates of
heteroatoms
A list of these coordinate, secondary structure, sphere, cylinders files that were created by the auxiliary programs are inventoried in the following files: 1I8F.atoms -a list of files containing balls (.sph)
These files control what gets drawn in the interactive ribbons display. For example, if you remove the name 1I8F_E_pro5.pdb from the 1I8F.coords file, then chain 5 will no longer be displayed in ribbons. STEP TWO Change the ribbon coloring scheme. Go to the Edit menu with right mouse button, drag to Ribbon Style Panel and release the mouse button. You will get a new window with many options. Use right button to drag open the Sequence Color window and select "chain" to color by chain. If you wish, there are many other interesting options you may chose to explore. STEP THREE Display Arg29 sidechains from entire heptamer. You need to create a separate PDB file that contains coordinates of the 7 arg sidechains. The easiest way to do this is to type: grep 'ARG . 29' 1I8F.pdb >arg.pdb Then, to make ball-and-sticks type: atom-model arg.pdb 1I8F.model This will create the files arg.sph and arg.cyl. It will also automatically append the name arg.cyl to the 1I8F.bonds file then add the word arg.cyl to the 1I8F.atoms file. To update the graphics window, click on the File menu and select Re-Read Data, then Everything. You should see the seven arginine side chains pointing to the center of the heptamer as shown on the right. STEP FOUR Convert the O format map (also known as dsn6 or brick format) for use in Ribbons. The Omap must first be converted into triangles using the auxilliary program "facets." Unfortunately, facets only works on SGI machines, so you will have to rlogin to an SGI (e.g. Harker) and in a unix window type: facets mask.omap mask.tri It will take a minute to write out the triangle file (mask.tri).
You will then have to make a file called 1I8F.polys and write the name
"mask.tri" on the first line. Then go back to the file menu in the
ribbons window and select Re-Read Data, then Everything. You should
see the mask appear, covering the molecule, as in the figure on the right.
Orient the model to show a slice through the middle of the heptamer. This will involve knowing the function of the mouse buttons. See the mouse button key on the left. First zoom back using the left mouse button and dragging. Then rotate the heptamer about the X-axis so that the 7fold symmetry axis is vertical (middle mouse button). Then use the Z Translation to get the cut-away effect. You may also wish to change the Z Thickness. Save the orientation by going to the File menu and selecting Save All Three Below. It will create 3 new files, recording the orientation, colorscheme and other choices you have made during your ribbons session. In the event that you have to end your ribbons session, your current orientation, colors, etc. will be automatically read in and applied to your model. STEP SIX Adjusting the color scheme. Change the background to white using the View menu and selecting B/W background. Changing the bond color to white is easily done using the bond control panel selected from the Edit menu. More difficult is to change the color of the individual atoms or chains. Hopefully, you won't need to do this, but if you do, then you must edit the .sph or .ss files. In the .sph file, you need to change the penultimate column. The numbers in this column correspond to different colors, for example, number 1 is red, 2 is green. Just change the number to correpond to the color you desire. If you want to customize the color of the individual monomer ribbon chains, then edit the hb column and change the letters to the number of the color you desire...and you must do this for each residue. What a thrill! If you wish to save your image and you are using a DEC alpha, I suggest that you use xwd. If you are on an SGI machine, you can use the save image option under the files menu. Remember to hit the Print Screen button afterwards. The output is an rgb file which can be converted to other formats using ImageMagick. This Print Screen option doesnt work on DEC alphas.... there is a bug, sorry. Be happy, your figure is finished! And only the last part was painful! |
Ribbons window obtained in step one.
Ribbons window obtained in step two.
Ribbons window obtained in step three.
Ribbons window obtained in step four.
Mouse Controls Key
Ribbons window obtained in step five.
Ribbons window obtained in step six.
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