To make a dimer from a monomer using crystal symmetry.

• If the pdb file has a cryst1 line in it, with unit cell dimensions and space group information, Swiss PDB viewer may work. Or, you can manually pick the correct space group.
  
  this file spo0a.pdb worked in swiss pdb viewer version 3.6b_3
  this file dctd.pdb worked in the swiss pdb viewers that are installed in the lab
• Open the file
• tools
  • build crystallographic symmetry
  • find number 154 (if you are using spo0a.pdb; number 23 if you are using dctd.pdb)
  • click on the red entry - to activate all of the listed symmetry operators, or the black entries under the red one to individually draw specific symmetry related molecules
• Now, in the layers info panel identify each by turning them off, and selectively close all unwanted layers.
• Then, select all residues, and make a new pdb file containing the dimer as in the overlay exercise.
• If not, use 'O'. (self-extracting zip file for nt version as of 9/2000; see 'O' site for details, but:
  for our class you could download the file into c:\nt_o, and execute it to install the program)
  
  Important Note - for some reason Swiss PDB Viewer does not always draw the symmetry related molecules in the same unit cell as your opening structure; this can be a real headache - but you can move them using the 'translate along unit cell axis' function. Unless you understand symmetry for the particular space group you are working in, this can be tricky. 'O' has another ability which I like very much, so consider the following way of working with symmetry related molecules.
  
• You type the black text; red is for your information only.
• Start 'O' by clicking on nt_o.exe
  • not the install file I gave you, but the result of having run it to expand the zip file into all of the needed files for 'O'. If you put it in c:\nt_o  and expanded it there, there is a link to the nt_0.exe program in the course software list, and you can always find it by start-run-explorer or using the ws_ftp local directory browser function.
  • s-a-i spo0a.pdb mod1
    • s-a-i stands for sam-atom-in, which means read a pdb file into the program
      spo0a.pdb is the first argument of the s-a-i command, and it is the pdb coordinate file
      • the assumption is that the file is in the nt_o.exe folder - if not, give the path
    • mod1 is what I chose for the name of the molecule (we can load more than one, so each has to have a unique name)
  • mol mod1 ca ; end
    • mol mod1 means use molecule called 'mod1'
    • ca means draw the alpha carbon backbone
    • ; means end the command string
    • end means perform the operation
  • cen-at a7
    • command for centering the view on residue chain a number 7
  • adjust zoom
    • this is an instruction to you, not a command for 'O'. To adjust the zoom level, you need to click the middle mouse button if you have one, and drag up or down. If you don't have one, then click on the menu pulldown list, click on the 'fake dials' item; click on its left top small rectangle to keep it open. You may move it to another place on the screen by clicking and dragging the top right small rectangle. To work any of the dials, click on the desired function and slowly drag left or right within the box defining the function. To the left zooms one way, to the right zooms the other.
  • sym-set mod1 59 59 67.9 90 90 120
    P3221
    • sym-set is the command for setting the unit cell dimensions and angles, and entering the space group for which known symmetry operations can be used in later functions
    • sym-set requires several arguments
    • three numbers - the a, b and c unit cell dimensions in Angstroms
    • three numbers - the angles of the unit cell in degrees
    • an alphanumberic text - the name of the space group
  • use 'center on atom' tool to click and center on an atom of the extended helix
    • open the menu - user menus item
    • left-click on the 'center on atom' function
    • left-click on an atom of the model
    • the view will now be focussed and centered on this atom
    • pick a point close to the dimer contact area, as we will be searching for symmetry molecules near that point
  • sym-sph 5 sym
    • means locate and draw symmetry related molecules within 5 Angstroms of the current focus point, naming them sym1, sym2, ...
    • another way to see symmetery molecules is the sym_obj command (no arguments); however, this one does not create a new molecule object like the sym-sph command
  • mol sym1 ca ; end
    • using molecule sym1 (assuming that is what you created with sym-sph) draw the backbone
  • do you have the dimer? - just a question for you
  • s-a-o
    • to write a pdb file for the symmetry related molecule, give a name you want, identify which molecule you want to use (sym1 in the example above), and answer other questions with default answers. You can select a subset of a structure if you want, and include or exclude B-factors, etc. Don't worry about these details yet.
  • del mod1 sym1
    • to remove the molecules from 'O'
  • s-a-i both pdb files back in to make sure you have the correct pdb files; use two unique names and mol name ca ; end to draw their backbones (or, 'zone' instead of 'ca' will draw all atoms)
• use swiss pdb viewer to join the molecules into one pdb file