Third exercise with RasMol: Saving image files

Remember the procedure:

1. Name a Folder with your name and place a copy of RasMol in it. (RasWin for Windows, RasMac for Macintosh).

2. Get a protein file in pdb format from the Protein Data Bank.

3. Click on "Download/Display Structure".

4. Scroll down, if necessary to "Download the Structure File"

5. Choose compression: none, file format: PDB. Control-click to download into your RasMol folder.

6. Check to see a file called "****.pdb" in your folder.

7. Now open RasMol.

8. Arrange the 2 windows so that the white command line window is in the lower left-hand of the screen. It should be short and wide. Make the graphical window large. Allow a few lines of text in the bottom of the command line window to be visible.

9. Begin typing: load ****.pdb

Notice that the command line window will remain in the background while you are typing. As long as you can see what you are typing, it is never necessary to switch back and forth between the windows.

10. After hitting Return, you should see text about the file appear, and the molecule should appear in the graphical window. An online RasMol help file exists, but only for version 2.6. It is largely accurate for the current version.

11. You can change the molecule by using the Display and Colors Menu. Try it out.

12. You can also use the command line, which is extremely powerful once you learn a little.

13. For example, I prefer a white background. (It saves on black ink also).

Type: background white

(Commmands are always followed by Return).

14. There are 2 ways to incorporate a RasMol image into another document:

1. Copy and Paste
2. Write a file, then insert it

15. For the first method, open a document that you want to insert the RasMol image into.

16. Go back to RasMol. Type: select all    (or select it from the "Edit" menu)

17. From the "Edit" menu, select "Copy" or use the keyboard commands.

18. Go back to your document and "Paste"

19. Method 2. One way to make the image look better is to increase the size of the RasMol image window. Drag the window to the upper left, then re-size it to the lower right, by dragging the corner.

20. Use the "Export" menu. For Windows, the BMP file format should work, but it might not function in 32-bit RasMol. For Macintosh, PICT files will work. You can try GIF also.

26. To use the Command line, type: write pict ****.pict (or write bmp ****.bmp)

27. Now go back to your document and use the "Insert" menu.

28. Remember to save a script file. Type: script ****.spt

29. If you have a problem with a file that you cannot use, send it to me. I can convert one filetype to another (e.g. jpg).