A short primer on how to use MidasPlus - Table of Contents

Based extensively on the tutorial created by Bryan Jones, Biomolecular Structure Center, University of Washington. Thanks, Dr. Jones!

Important Notes:

• Some of the MidasPlus commands in the tutorial include filenames that are links. You will need to save a file via the browser before using it in a MidasPlus command. Also, make sure you put the file in the directory from which you are running MidasPlus.

• The tutorial is geared toward Silicon Graphics users. On other platforms, the interface may differ slightly from the descriptions in the tutorial, although the commands are generally the same. "RGB" files and the image tools that manipulate them are also SGI-specific.

For general information regarding MidasPlus, check out the UCSF MidasPlus page. At the UCSF site, there are a number of images, with detailed instructions on how they were made. What follows below is simply the appropriate use of the commands within and concerning MidasPlus, and therefore, little in the way of creative assistance regarding images. For more help, check out the other http-based MidasPlus tutorial.

1. Starting MidasPlus

• starting MidasPlus
• general description of the window
• exiting MidasPlus

2. Viewing Molecules in MidasPlus

• on-line help
• various simple commands for manipulating the display

  chain

  display & ~display

  show & ~show

  color

  vdw (& vdwopt)

  savepos & reset

  push & pop

3. Modeling Utilities within MidasPlus

• atom picking & labeling
• distance & angle measurements
• replacing or altering amino acids

  swapaa & addgrp (for alteration of covalent structure)

  rotation & watch (for alteration of noncovalent structure)

4. Graphical Rendering in MidasPlus

• ribbonjr
• neon & conic
• rainbow
• label3d
• noeshow

5. Other Useful Commands in MidasPlus

• alias
• adding your own color
• set & ~set
• record & source
• command recall & editing

6. Displaying More Than One Molecule in MidasPlus

• viewing
• superposition

7. Finishing and Saving a MidasPlus Session

• writing out PDB files for the altered orientation
• saving the session for future work

8. Programs Outside of MidasPlus

• dms & esp (solvent accessible surface)
• image tools

...and programs which run either in or outside of MidasPlus

• ksdssp
• conic
• neon
• ribbonjr

An appendix is included that has a lot of relevant information (colors, chemical group names, lists of programs).