PyMOL Info/Commands

Links

• PyMOL Home Page
• User Guide
• Nuccyl - Script which allows PyMOL to draw a particular representation of Nucleic Acids, similar to Ribbons

Manipulating the View

• zoom
  • Calculates a pseudo-optimal zoom level for your molecule. This is based on the current view, so rotations and other manipulations might cause the image to be clipped.
• zoom complete=1
  • ensures everything will fit in the view
• full_screen on
  • Go into full screen mode. Alternately, full
• full_screen off
  • Get out of full screen mode
• bg_color white
  • Have fun with the background color
• origin selection or ctrl-shift-middleclick
  • Change the origin of rotation
• center
  • centers the molecule in the frame
• center selection
  • center about a selection, useful in conjunction with origin
  • you can also use cent, and selection can be a molecule name
• set_color color_name, [ float, float, float ]
  • Allows you to set your own custom colours beyond those that are predefined
  • Standard RGB argument, except values are floats from 0.0 -> 1.0

Ray Tracing

• ray
  • This will ray trace the current scene for you
• set ray_trace_frames=1
  • This will turn on ray tracing for all frames in a movie. To turn it off, set it back to 0
• set antialias=1
  • Turn on antialiasing for ray tracing, makes things look much smoother and better
• set orthoscopic=1
  • This makes the OpenGL view and the raytraced view match up in space
• set ray_trace_fog=0
  • Supposedly better for light backgrounds, give it a whirl

Selecting Things

• select selname, name x+y+z
  • selects all atoms named x, y or z into the group "selname"
• select selname, resn x
  • selects all residues named x into the group "selname"
• select selname, resi 5
  • selects residue 5 into the group named "selname"
• select selname, resi 7-10
  • select a range of residues
• select selname, resi 14+16+18
  • select individual residues
• select bases, name c2+c4+c5+c6+c8+n1+n2+n3+n4+n6+n7+n9+o2+o4+o6
  • selects all the atoms of the 4 rna bases (except hydrogens) into the group "bases"
• select backbone, name o1p+o2p+o3p+p+c1*+c2*+c3*+c4*+c5*+o2*+o3*+o4*+o5*
  • selects all the atoms of the rna backbone (sugar and phosphate) into the group "backbone"
• select sugar, name c1*+c2*+c3*+c4*+o2*+o4*
  • selects all the atoms of the 4 rna bases (except hydrogens) into the group "bases"

Calculating, Fitting, etc

• Ctrl-Shift-Left Button to select the atom "lb" and Ctrl-Shift-Right Button to select the atom "rb"
  • dist from the command prompt will give you the distance between them
  • MacPymol uses different combinations to select atoms - try double-right-clicking on atoms
• fit model1, model2
  • Superimposes model1 onto model2 and calculates the rmsd - only works if the models have the exact same atom composition
• pair_fit selection1, selection2
  • Superimposes selection1 onto selection2 and calculates the rmsd - this works on the designated atoms subsets in a model, useful for comparing structures with different sequences, etc (ie select only phosphate or C-alpha atoms)

Output

• png filename
  • simply outputs a png image of the current scene to the specified file

Movies

• load structure.pdb, mov, x
  • this loads the file structure.pdb into the movie "mov", at frame/state x (where x is a number >=1). It is not necessary to include x, by default it will simply load into the next unused frame
• mset 1 -30 -1 -45
  • Specify the frames for the movie. The above command means the movie will display frames 1->30, then 29->1, then 2->45
• mpng moviename
  • this will output each frame of the movie as a png file with the base name "moviename" to the working directory

Scripts

• @scriptname
  • This will run a script from the specified directory
• rnaview1.pymol
  • Make your RNA look pretty, with colouring based on residue type. First load the RNA, then run this script.
  • Uses a cartoon-style backbone
• rnaview2.pymol
  • Make your RNA look pretty, with colouring based on residue type. First load the RNA, then run this script.
  • Uses sticks for the whole molecule
• movieload.pymol
  • Load a directory full of PDB files into a movie. You edit the first line to be the correct directory for your files.

Patrice-Style Representations

• hide all
• show cartoon
• cartoon loop
  • This sets the cartoon type to "loop". If you want to use "tube" instead, then you should use "cartoon_tube_radius" below as well
• set cartoon_smooth_loops=0
  • This allows the path of the cartoon to follow more or less the actual path of the backbone, and not be smoothed out
• set cartoon_loop_radius=2.5
  • Change this value to taste
• set cartoon_loop_quality=100
  • Make things prettier, to taste