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Rasmol tutorial Controlling the Rendering

One of the basic tasks here is to simplify the representation in specific ways to reveal various characteristics, interactions, etc. First strip away most detail to visualize the global fold and secondary structure of the protein. Click on the Rasmol Command Window and type. "restrict protein" this command cuts away all atoms except protein atoms "select DNA" selects DNA Pull down the display menu and set the display to ball and stick. Note that this changes the rendering only of the selected atoms (in this case, the DNA). "color blue" changes the color of the selected atoms to blue. Try green, red, cyan, etc. "select hetero" selects non-DNA, non-protein atoms Pull down the display menu and set the display to spacefill. Now you can see the oxygen atoms from water molecules. In an x-ray diffraction experiment, hydrogen atoms are generally not observable, so they are left out of the coordinate file. "color red" changes the water oxgen color to red Let's take a look at the DNA in the absence of everything else. "restrict DNA" Pull down the display menu and set the display to spacefill. "select c or g" "color red" "select a or t" "color green" Pull down the display menu and set the display to sticks. "restrict t2, g3, c114, a115" turns off everything but a dinucleotide step (i.e., two base pairs plus the backbone) "select all" "color red" "select c114" "color cyan" "center g3" sets the rotation center to residue g3

Measuring distances
Click the [Distance] button in the Molecules Window to toggle that function on. Click on any two atoms of the dinucleotide. Note that the distance between them pops up in the Command Window. If you toggle on [Keep labels on screen] in the Molecules Window, the names of the atoms and the distances between them remain on the screen. [Alternate method: in the command line type "set picking distance"] Click on the [Distance] button a second time to toggle that function off.

Measuring angles
A bond angle is determined by the relative positions of three atoms. Click the [Angle] button in the Molecules Window to toggle that function on. [Alternate method: in the command line type "set picking angle"]

Click on any three atoms of the dinucleotide. Note that the angle between them pops up in the Command Window.

Measuring torsion angles


A torsion angle is determined by the relative positions of four atoms. Phi and psi are torison angles within peptides and proteins. The conformation of each amino acid residue is characterized by phi and psi. Click the [Dihedral] button in the Molecules Window to toggle that function on.[Alternate method: in the command line type "set picking torsion"] Click on any four atoms atoms, which are bonded together linearly. Note that the dihedral angle relating them pops up in the Command Window. The dihedral angle relating four atoms in a plane is zero.

Studying Interactions between DNA and Protein.


Now let's study how this protein binds to the DNA. "select DNA" "color white" Set display to Spacefill. "select protein" Set display to stick. "select protein and backbone"

Studying Hydrophilicity, Hydrophobicity and Amphiphilicity

RasMol can show locations of polar and non-polar residues, and tell you if -helices are amphiphilic. "select protein" set display to stick "select backbone" set display cartoon "select hydrophobic" selects all hydrophobic residues "color red" "select polar" selects all polar resides "color cyan" "select arg, lys, asp, glu" selects charged residues (not histidine, which is sometimes charged). "color blue"

Finding Hydrogen Bonds


"hbonds" calculates hydrogen bonds. The program doesn't really know where the hydrogen atoms are, so it has to make some assumptions about them. "hbonds on" turns them on "hbonds off" turns them off This function seems to work within a protein but not between the protein and a ligand.

Rasmol Help
"help commands" gives a list of commands. "help colour" [or "help color"] gives a list of available colors. "help expressions" and "help sets" gives partial lists of expressions for selecting or restricting atoms. Some useful expressions are given here. Rasmol Expressions (note there are two types of wildcard; * & ?)
select expression select all select hydrophobic select polar select alpha select helix select sheet select ligand select water select DNA select at select cg select 14 select 14,21 select 14-21 select 14-21,35 select atomno=1259 select arg select arg43 select arg43.ca select arg.ca select *.cb select arg.c?? select arg43.* select *.?e? result selects everything selects all hydrophobic resides selects all polar resides selects all -carbons selects all resides in -helices selects all resides in -sheets selects ligands selects water molecules selects DNA atoms selects adenine and thymine selects cytosine and guanine selects reside number 14 selects reside numbers 14 and 21 selects reside numbers 14 through 21 selects reside numbers 14 through 21 and 35 selects atom number 1259 selects all arginine resides selects arginine 43 selects C of arginine 43 selects all C atoms of arginines selects all C atoms selects all carbon atoms of arginines elects all atoms of arginine 43 selects epsilon atoms of all residues (the 2nd ? is required because some residues have e1 and e2)

select within (8.0, ser) selects all atoms within 8.0 of all serine residues select within (6.0, 14-21,35) selects all atoms within 6.0 of residues numbers 14 through 21 and 35

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