Making Slides and Pictures
There are many ways to create molecular graphics images for publication and projection. Below is a set of procedures to get you started.
Mark Harris has a tutorial on image manipulation available.
Checkout the Biomedical Communications web page. They have a lot of general information on computer-generated slides and
will accept floppy disks for making slides.
If you would like a classy background to work with here is a sampling.
If you are making a seminar presentation try Microsoft Powerpoint on the Mac or PC.
To import your molecular graphics images (usually SGI RGB format) open the image in GIMP, go to "Image -> Index" in the pull-down menu, and generate a 256 color palette; then save the image as a GIF format. This GIF can be FTP'ed directly to the Mac or PC and imported into Powerpoint.
Steps for making slides and pictures using CSB applications:
- Save individual images with either white or black background.
- Assemble your picture from the saved images.
- Label your picture
- Make hardcopy (slide, paper, transparency) of your picture.
Step 1 - Save individual images with either white or black background.
A. Set color of application background.
GRASP, O, MidasPlus, Ribbons have black as the default color
- For BLACK background (use cyan, yellow, green, magenta, white foreground NOT red, blue)
- For WHITE background (use blue, red, green, magenta, black foreground NOT yellow, cyan)
- Use the "panels" option of the main menu to get the "options" menu.
- In the "options" menu choose "background"
- In the "background" menu turn the "Background Box" option off
- Press the "background On" button and fill in a colour in the "enter background
- In the Midas window, type:
set bg_color white
- Click View pull-down menu
- Click B/W Background command
B. Smooth Image with Antialiasing
- Click RIGHT button to get menu
- Click Miscellaneous
- Click AntiAliasing (Polygons)(One Shot) and wait about ten seconds while the images are accumulated. You will then
see your image much improved.
You can save this image from within GRASP or snapshot (import on DEC's) it as described below. To save it:
- Click RIGHT button to get menu
- Click WRITE command
- Click RGB/Snapshot File
- Give the name of the filename.rgb in the winterm and wait about 10 seconds until the winterm re-appears.
- Depress the F5 key
- Choose the zbuffer (second option)
- In the same directory where you launched Midas type:
echo 'antialias 2x2' > conic.cf
- Then when you run conic or neon in Midas use the option:
(This can be slow, so get your image correct before using this option).
(Here you must save the smoothed image, it won't display interactively).
- Pull down View menu
- Click on Antialias Image and choose the number of images you want to accumulate. (The more the better,
and more time consuming.)
- Pull down File menu
- Click on Save Image
- Type the path and filename.rgb in the Selection box
- Press the Print Screen key and wait for the 'finished' message.
Your smoothed image is now in filename.rgb
C. Save image using snapshot or import
In an IRIX UNIX window type:
- When the snapshot icon appears, put the cursor over it, hold down the ALT key and RIGHT button and click the "Move" command. Now move the icon out of the way.
- Place the cursor over the snapshot icon, hold down the ALT key and MIDDLE button, drag the cursor to the upper left corner of the area you want to
snap, simultaneously hold down the LEFT button and drag the rubberband to enclose your image.
- Hold the cursor over the snapshot icon and hold down the RIGHT button to click on the appropriate "save" command.
In a DEC Alpha UNIX window type:
import filename.[ext] (Where "ext" is the format of the saved image, e.g. gif, sgi, tiff)
- Place the cursor (now a cross) over the image, hold down the LEFT button, drag the cursor from the upper left corner of the area you want to
snap. When you release the button an image file, "filename.[ext]" will be created.
Step 2. Assemble your picture from the saved images
A. Set the display color
- In a UNIX window type either one of the following:
xsetroot -solid black
xsetroot -solid white
B. Assemble the image
- Draw a new snapshot rubberband in a clean area of your screen of the size
and shape you want your picture to be.
For each of the images that you will combine in your picture do the following:
ipaste -n fileneme.rgb &
- When the image appears, hold down the ALT key, move the cursor over your image and hold down the RIGHT button to click the "move" command. Then move your image with the mouse to it's position within your
- When your images are assembled within the rubberband save the composite
picture using snapshot.
Step 3. Label your picture
The preferred method is to use GIMP. The description of ilabel below is valid but inferior.
Ilabel allows you to create labels on a .rgb image. You can then save the labeled picture or save the labels in a separate
file for later viewing and editing with the .rgb picture.
ilabel -o filename.lbl filename.rgb
where filename.lbl will be the file containing labels and filename.rgb is your picture file.
- With the cursor over the image, hold down the RIGHT button and click the "Show Defaults" command. This will pop a dialog box where you can set the Font, Size, Justification and Color of your labels.
- Place the cursor over your image where you want the first label, click the RIGHT button, and start labeling.
- Click the RIGHT button in a new place to start a new label.
- You can move the labels later using the MIDDLE button.
- When done labeling you can save the picture by holding down the RIGHT button and clicking the Save Image command. If you click the Exit command the labels will be saved in the file, filename.lbl.
- To later edit the labels, type:
ilabel -i filename.lbl filename.rgb
Steip 4. Make hardcopy (slide, paper, transparency) of your picture.
Making 35 mm slides on the Focus Slidemaker (Imagecorder)
NOTE: Make sure your image files have world read access!
Two Imagecorders are installed, one is attached to csbile and the other to csblys.
- Load film in the 35 mm camera.
- With the Imagecorder on advance to first film frame with shutter button.
- Set film selector knob to the 'B' position.
- Insure that the Focus machine is on and displaying the "Ready" signal.
- You may want to change (or check) the Image Options settings before continuing!
- From csbile or csblys type:
- Highlight the Focus printer in the list in the dialog box that appears.
- Choose More Options to set your preferences (e.g. 35 mm).
- Save the Options
- Enter the filename (full path) of your picture in the form box labeled Files to print: and click the Print button.
Polaroid Color Film Recorder
Attached to GLAZIER is a Polaroid ProPalette 7000 Film Recorder.
Instuctions for using the film recorder are found at the links below.
Please follow these instructions as written. Modifiying parameters on
the film recorder software can cause problems. The only items that
you need to modify are stated in these instructions. If you do
modify other parameters, make sure you change them back before exiting.