Using RASMOL for Molecular Grafix LiteDuring this course you will need to look at the macromolecules we'll be discussing withsome appropriate molecular graphics program. If you're whiz at Unix-based systems and arecomfortable with downloading PDB-files from the net, stop here: you don't need this handout. But if you stumble awkwardly on electronic iceskates, as I do, then you may benefit from alower-level molecular graphics package. Currently, there are two such packages that run well onPCs and Macs, and can do almost as much as the fancy Unix-based programs can. RASMOL,written by Roger Sayle at the University of Edinborough, is excellent and user-friendly. I haveset up RASMOL on the Feldberg server and Hughes server in the library basement, in a folderlabeled "Biochemistry 104." You should go down there and play with it soon, because you willneed to use it to examine some of the proteins and nucleic acids we'll be reading about in class. You do not have to be an expert at RASMOL, but you should know a few basic things.Windows. RASMOL maintains two windows -- the Graphics window where you actuallylook at the molecule, and a Command window, where you can type in explicit manipulations,such as coloring atoms or residues, rotating about axes, or labeling atoms, for instance.Menu Bar. At the top of the graphics window there is a menu bar that lets you do most (but notall) things that you might want to do -- open files, choose various color schemes, put ribbon-cartoons on the image, get help on specific commands, etc. To bring up an image of wild-typelysozyme, for example, go to the File menu, click on Open, and from the list of PDB files,choose lyswt.pdb. The image of lysozyme will appear, and you can move it around with themouse. Experiment with the left and right buttons. Play.Renderings. There are two basic ways to render the molecules: as bonds or as spheres. Thesecorrespond to the commands wireframe and spacefill, respectively. When a file first comes upit is displayed as a thin wireframe. You can change this in several ways; a few examples ofcommands to write in the Command window should give you the idea:wireframe 0.3 this makes the bonds 0.3 angstroms thick, easier to seespacefill this gives each atom its van der Waals radiusspacefill 0.7 this makes each atom a sphere of 0.7 angstrom diameterspacefill off removes the spheres you'd previously drawnwireframe off same dealBchem 104 handout -- RASMOL, page 2Colors. There are lots of ready-made color schemes, and you can easily create your own. Initially files come up in the "CPK" conventions, with carbon grey, oxygen red, nitrogen blue,sulfur orange, etc. The colour command (note classy British spelling!!) is very useful.colour red colors the currently selected atoms redcolour ribbon white colors the backbone ribbon whitecolour labels cyan colors the atom labels cyanSelecting atoms. This is the most important, and also the trickiest, thing to understand: theselect command. When you initially load a file, all the atoms in the structure are automaticallyselected. But you might want to look only at the backbone, or you might want to color only thealpha-carbons purple, etc. To specify atoms, you have to use select. This can be tricky becausethe command is rigorously boolean. Here are some examples:select backbone select not hydrogensselect *.ca, LYS27 all the alpha-carbons and all atoms in Lys27.select *.ca and Lys27 atoms that are in BOTH Lys27 and are alpha-carbons,i.e., ONLY Lys27.ca. (Better: select Lys27.ca)select backbone and *.cb atoms that are in backbone and are beta-carbons, i.e.,nothing!!select backbone, *.cb atoms in backbone and all beta-carbons.select U204.P the ribose phosphate of base U204 in an RNAIt's important to realize that select does not by itself change the display. It won't add or removeresidues from what you see on the screen. It simply sets things up for the next command to actupon. Here are some examples of this:select backbone these two commands together are needed to color every atomcolour red in the backbone redselect cys and (*.cb, *.sg) makes the $-carbons and the (-sulfur atoms of allspacefill .7 cysteine residues spheres of 0.7 angstrom diam.select not backbone turns off the display of all atoms that are not inwireframe off the backbone. This can be done better by a restrict command: restrict backbone. (see below)select Arg19.C? colors only the carbon atoms in arg19 green, andcolour green displays them with 0.4 angstrom thick bondswireframe .4 (note use of single-character wildcard "?")select Arg19 and not hydrogen colors all but H-atoms in Arg19 greencolor greenBchem 104 handout -- RASMOL -- page 3Restricting displayed atoms. The restrict command is also very important, and you shouldknow how to use it with the select command. Restrict is used to specify which atoms areactually being displayed at any time. In contrast to a select statement, a restrict statementchanges the display immediately. The select command acts only on atoms that have already beendeclared in a restrict statement; a select on atoms that are not in the set of restricted atoms willdo nothing! Here are some examples:restrict * show all atomsrestrict not hydrogen show everything except H-atomsrestrict 12-43 show only residues 12-43restrict (not backbone) and (not hydrogen)shows only the non-H atoms of sidechains!Picking atoms with the mouse. Sometimes you'd like to know the name of an atom. (Forinstance, you might not know that a gamma carbon is called "CG" or that the ,-amino nitrogen ofa lysine is called "NZ".) You can easily find out the name and residue of a given atom on thescreen by clicking on that atom; the atom name then appears in the Command window. This isuseful if you want to color a particular stretch of sequence differently than the rest of themolecule. Suppose that the molecule is on the screen and you'd like to put a purple ribbon on acertain stretch of "-helix. You click on atoms at the beginning and end of the helix to find outwhat residues the helix spans. Say these come up Ser10 and Leu20. Then, the followingcommands will put a purple ribbon of 0.6 angstrom width on only that stretch:select 10-20 and backboneribbon 0.6 ("cartoon 0.6" makes a slightly different-looking ribbon) colour ribbon purpleA nice feature of RASMOL is that you can measure distances between atoms with the mouse aswell. To do this you have to first activate the distance monitor.