VMD User's Guide

a line between the two atoms with the distance drawn in the middle and a bit to the right. Thedistance between the two atoms is 2.94 Å, as compared to 2.93 Å in the paper; not bad. However,picking the distance between the FE and the C of the CO reveals a distance of 1.91 Åascomparedto 1.85 Å in the paper. The difference is that the structures in the VMD distribution are actuallypreliminary structures obtained before the final coordinates were determined.In order to experiment with more complex picking modes, consider the angle made by the Oof the CO with the FE of the heme and the NE2 of residue 93 (you can click on the atoms to findwhich ones are which). Using the Mouse menu, change the pick mode to “Angles”. This shouldcause the cursor to become a red crosshair. Click on each of the three atoms using the left mousebutton. After the third pick, a shallow angle will appear indicating an 8.71 degree angle betweenthe three atoms.Now load the intermediate star.pdb file which can also be found in the proteins directory ofyour distribution. Again use the Files form to do this. Both of the molecules will be loaded side byside. Go to the Graphics form and change the selection so it the same as the first, i.e. resname HEMCO or resid 64 93. The two molecules are almost atop each other, making it hard to distinguishthe two, so change the colors to simplify things.First, in the Graphics form, change the Coloring method to ‘Molecule’. Use the Selected Moleculechooser to change the mbco.pdb Coloring method to ‘Molecule’ as well. Open the Color form [§4.4.9]and scroll the Category browser down until the line ‘Molecule’ is visible. Click on it then clickon the line which says mbco.pdb. (Theremaybetwombco lines if the file had been loaded beforein this session.) Scroll the Colors browser up to click on ‘blue’. This should change one of themolecules in the display to blue.Next, click on the last line in the Names chooser, which says star.pdb. This time, choose ‘red’from the Colors chooser. The display should be much easier to understand. The myoglobin withthe bound CO is in blue and the intermediate state is in red. At this point it is easy to measurethe change in position between the two different states by using the middle mouse button to pickthe same atom in the two conformations.Once that is done, it is easy to point out one interesting aspect of the way VMD handles thegraphics. Go to the main form, select one of the two molecules, and press Toggle Fixed. Entertranslation mode and move the other molecule around. Notice that the number which lists thedistance between the two atoms never changes. That’s because the mouse only affects the way thecoordinates are translated to the screen image. It does not affect the real coordinates at all. It ispossible to change the coordinates in a molecule using the text command interface, or by using theatom move pick modes [§4.1.2]).By the way, unfix the molecules and do a ‘Reset View’ from the Display menu to reset everything.Load up the third structure, deoxy.pdb and give it the same selection as the other two molecules.However, color this one green. Pull out Nature v. 371, Oct. 27, 1994 and turn to page 740. Witha bit of manipulation you should be able to recreate the image that appears there.2.7 Some Nice RepresenationsThe following views are quite nice for displaying proteins and nucleic acids:selection: alldrawing method: tubecoloring method: segname (or chain)why? This show the backbone of the protein and nucleic acid strands18