Trouble Shooting. You typed a command, and what you expected to have happen, didn't. Call me? OK, but first do a little trouble shooting; that is, check for simple mistakes. Remember what I told you? "Computers are idiots; they always do exactly what you tell them to do." The computer didn't make a mistake, you did. So, when something doesn't work, check a few things:

• Look at the command you just typed. Is everything spelled right, including case?

• Are you in the proper directory? Type pwd to find out. You need to run Gaussian, for example, from the directory where the input file is, or else provide a path to the input file.

• Does the file you're trying to operate on actually exist? Type ls and look for it. Maybe you didn't name it what you thought.

• Is there an error in the file? Use less to check punctuation, spelling, cases, quotation marks, etc. If you find a mistake, use vi to fix it.

• Does your .bashrc contain the proper aliases, environment variables, and so on, to access the program you're trying to run? Again, check for spelling, quotation marks, equal signs, and the like. Check that you didn't accidentally add some extra lines, or delete some essential ones.

• I like to keep a backup copy of .bashrc. When you've got everything working right, cp .bashrc bashrc.bak. Then the next time you make a change and screw something up, cp bashrc.bak .bashrc and you can start over.

• Did you source the .bashrc after you edited it?

How Can I Make Spartan Print the Total Energy in Semi-Empirical Output ?

Damn the crappy Spartan manual. The manual for the old version is much better. When you set up the semi-empirical calculation, type in the box at the bottom of the pop up form: PRINTLEV=2.

You will automatically get a more verbose output, including the electronic energy, the core repulsions, and the total energy, all in hartrees.

What's a Ramachandran Plot ? A Ramachandran plot describes regions of more stable conformations of a protein chain in terms of backbone dihedral angles. Here's more detail.

Accessing Procheck. Procheck compares the geometry of a protein as contained in a Protein Databank (.pdb) file to such standards as the Ramachandran plot of backbone dihedrals. It creates extensive reports, including numerous graphics in the Postscript format. To use it, edit your .bashrc file to include:

# Procheck
export prodir="/usr/local/Procheck"
alias procheck="$prodir/procheck.scr"

Then run Procheck by typing:

procheck filename.pdb resolution

Resolution is the numerical resolution achieved by the crystallographers who produced the .pdb file. It can be found in the heading information in the file; if no resolution is given (for example, if the structure was determined by nmr), use any floating point number, say, 2.0.

Viewing Postscript Files. Several of our programs, including Procheck,write graphical output in the form of Postscript files. These have the extension .ps. They may be viewed on your workstation using a program called Ghostscript. Type:

gs filename.ps

and you will get a display of the graphic. Close the display by clicking the x in the upper right hand corner, and exit Ghostscript by pressing Enter. Ghostscript can also convert Postscript files to graphic file types that you can move to your PC and paste into Word and other Windows applications. Two examples:

For jpeg files:
gs -sDEVICE=jpeg -sOutputFile=filename.jpg filename.ps

For png files:
gs -sDEVICE=png256 -sOutputFile=filename.png filename.ps

After issuing the command, press Enter and then type quit. Typing:

gs -h