Building Gramicidin A
Save Positions
By now you should have positioned the protein as follows:
1. Switch to Move Molecule mode by moving the mouse into the graphics window and pressing the 8 key. The cursor should now have the form of a cross-hair.
2. While holding down the shift key, click on one of the protein atoms and drag the mouse. You should see just the protein rotating around the atom you picked. Try to align the axis of the protein with an imaginary line coming out of the screen, so that it's perpendicular to the membrane. If you accidentally rotate the whole scene instead of just the protein, type "display resetview" in the text console to get back to the original view.
3. Type "rotate x by -90" in the text console. Now you want to center the protein between the phosphate atoms of the bilayer. This time, click and hold on one of the protein atoms _without_ holding down shift. Move the protein up and down until it's centered.
4. Switch back to the orginal view with "display resetview". If the protein looks good, you can go on to the next step; otherwise repeat steps 2 and 3 above.
Now run this step to save your protein coorindates to a file.
Run this step! Continue
save_positions.vmd # STEP 4: Save Positions display resetview animate write pdb protein_move.pdb global popemol mol modstyle 0 $popemol lines mol modselect 0 $popemol "all"
