PyMOL in PHENIX

Author(s)

Starting PyMOL

Setting up your view in PyMOL

Useful PyMOL commands

Additional information

Author(s)

• PyMOL: PyMOL executables are kindly supplied by Warren DeLano for distribution in PHENIX.

Starting PyMOL

Normally you will start PyMOL in PHENIX after one of the PHENIX Wizards has finished. In this case if you click on the magnifying glass on the Wizard screen, and select one of the choices that displays a structure with PyMOL, then PyMOL will automatically be launched with the appropriate PDB and map files.

You can also start PyMOL by clicking on the PyMOL button on the PHENIX GUI. In this case you'll need to read in maps and models yourself. You can read in a model to PyMOL by typing

load overall_best.pdb

Setting up your view in PyMOL

Here are some simple controls that let you choose what you see in PyMOL, assuming that you have a model (pdb_1) and a map (map_1) or maps loaded.

• Click a few times on "pdb_1" you will see the model turn off and on. Same for "contour_1.5". Similarly "all" turns everything on and off, and "map_1" turns the unit cell box (which may not be visible in your viewer) on and off.
• To the right of "pdb_1" you will see buttons labelled "A" "S" "H" "L" and "C". Click on each one and you'll see what they do:
  • "A" : Actions. lets you recenter, delete the object, and more
  • "S" : Show. For a model you may want to show sticks for clarity.
  • "H" : Hide. Undoes show.
  • "L" : Label. Choose what labels to display
  • "C" : Color. Choose colors.
• The little table in the lower right of the PyMOL display window shows what each mouse button does. If you have a 3-button (2 buttons and a roller) mouse, then hold the left button down and move the mouse to rotate; right button down and move the mouse to change the size; both buttons down and move the mouse to move the center.
• If you accidentally click the wrong buttons and some new object appears on the screen that you do not want, click on the "A" botton for the new object and select "delete" to get rid of it.

Useful PyMOL commands

Here are a few useful PyMOL commands that you can type in the PyMOL window or in the PyMOL Tcl/Tk GUI window.

• Read in a pdb file named "overall_best.pdb":

  load overall_best.pdb 

• Read in a xplor-style map named "map_1.xplor" and contour it at a level of 1.5:

  load map_1.xplor
  isomesh contour_1, map_1, 1.5
   

• Create a new set of contours at a level of 2.5 for a map called "map_1" that has already been loaded:

  isomesh contour_1, map_1, 2.5
   

• Get PyMOL help;

  help
   

• Get PyMOL help on the command "isomesh"

  help isomesh
   

Additional information

You can get the documentation for PyMOL at pymol.sourceforge.net/html/