To install Molmol get it 's two installation files from the source web site or the 3/8/2000 version at our class pub ftp site.

Place the  two files in a folder called c:\molmol

execute them by clicking on them in ws_ftp or explorer

• which you can run by
  • start
  • run
  • explorer
• or by opening a command window
  • cd c:\molmol
  • dir (to see the file names)
  • execute them by typing
    • filename1
    • filename2

Now, delete the two installation files - so you don't accidentally run them again.

The help manual can be accessed by running molmol.exe and under help click on viewer, and select browser and netscape.

Then close Molmol. From now on it should know to use netscape to open the help items you click on under help.

To determine the average structure from a set of NMR models, as in the file 1DJM (shift-click and save it locally; its big - 4.5 MB) do the following.

In Molmol

• file
• read molecule
• pdb

On the right hand side under selection click mol

• you'll see a number of models have been read into the program
• and all are selected

click under the select mol window

Then

• edit
• molecule
• mean structure

now look under select mol again

• select all the molecules except mean
• click on 1
• shift click on last one above mean
• close

Now,

• edit
• molecule
• remove

this deletes all but the mean from the programs scratch space

next

• select mol
• click on mean
• close

next

• file
• write molecule
• pdb
• whatever name and folder you want

and finally

• file
• quit
• no or yes -
  • select the no button if you don't want the program to return to this exact state the next time you run it;
  • select the yes button if you want the program to return to this exact state the next time you run it.
  • note that you can file write dump at any time to save a 'dump' of the current state, and then file read dump to restore it at any time. This is analogous to 'write script' in rasmol.

Now you can use Swiss PDB viewer or other program to superpose the real models on the average structure, writing down the rms deviation for the superposition.

Then, select the model that is closest to the average for use to represent the entire set of models in your Chime page.