Insight II Notes: Superimposing Structures

After specifying one set of atom pairs, you can click execute. Then you can add more set of atom pairs to the "list of atoms to superimpose" by typing in another specification and clicking on execute again. Once you have completed the entire list of atoms to superimpose, then click on the box next to End Definition and click execute, and the Source will be superimposed onto the Target.

If you want to superimpose a range of atoms or residues, or all atoms of the entire molecules, the two molecules MUST have an identical set of atoms. Only then will the program know which atoms to superimpose. Therefore, if you have two different conformations of the EXACT same molecule, you can easily superimpose these conformers. But if you have a different amino acid sequence, you can only superimpose residues that are identical, or you can superimpose backbone regions or individual atoms.

After superimposing two molecules, BE SURE THAT YOU ARE CONNECTED TO THE WORLD! IF you move just one molecule, you will obviously lose the relative orientation of the molecules. Also, the actual RMSD value is reported in the textport (your unix shell from which youstarted InsightII). This RMSD value can tell you how well the atom pairs superimposed.

Calculating an average minimized structure

1. Load all molecules into InsightII. Superimpose the molecules or orient them in the positions from which their average structure should be calculated. Fix/Fix/Fix potentials, partial charges, and formal charges.
2. Save each structure (use Molecule/get) as a Biosym-format file. Use a unique name for each structure. The files that will be created will have a suffix of .car
3. In the unix shell, concatenate all files:
   cat file2.car >> file1.car
   cat file3.car >> file1.car
   cat file3.car >> file1.car
   etc.
   
4. Edit you "master file of all structures" (in the example abbove, this would be file1.car).
   See the example file1.car file for calculating an average structure. To summarize, this file starts with a header:
   !BIOSYM archive 3
   PBC=OFF
   
   then has a comment line and date line for the first structure:
   comment line
   !DATE Thu Mar 20 14:47:04 1997
   
   Then lists the atoms,
   then ends with TWO "end" lines:
   end
   end
   
   then has a comment line and date line for the second structure:
   comment line
   !DATE Thu Mar 20 14:47:04 1997
   
   Then lists the atoms of the second structure,
   then ends with TWO "end" lines:
   end
   end
   
   etc.....
   
5. You must do the next step from a InsightII-initialized shell:
   
   • Type more /etc/cshrc.local and locate the line in the file that specifies something like "source /remote/model/biosym/cshrc". Type in this command.
     
   • Start InsightII, and exit InsightII. Your shell is now initialized for InsightII.
6. Type seqtodir file1.car, where file1.car is your "master file of all structures". A new file called file1.card will be created. Rename this file to file1.arc.
7. Start InsightII. Recall one of your structures.
8. Start Analysis (click on the Biosym Icon, and select Analysis).
9. Click on Trajectory/get, and get your file1.arc file.
10. Click on Trajectory/conformation, and select average. The average structure will appear!
11. Save this average structure.