Some distributives (gentoo, openSuse, etc.) contains default Pymol  without vmd molfile plugins. By the way these plugins are essential because give an ability to open trj, xtc, cube and other different useful file formats. Here is step-by-step instruction to compile pymol-1.4.x on openSuse 12.1 but I suppose it might work on other distributives as well.

  1. Download pymol sources from sourceforge: pymol-1.4.1
  2. Unpack it and read in INSTALL file what packages are essential:
    «Note that you must have OpenGL, glut, libpng, tcl/tk, python,
    freetype2, and Pmw already installed on your system for this to work.»
  3. Check the file layer3/Executive.c and find the line witch includes ce_types.h. It might be:
    Correct if it differs!
  4. Open file and uncomment everything related to VMD molfile. There are 3 places you should uncomment!
  5. Run:
    $>python build
    $>python install
    $>python install
  6. If something wrong, clean builds with command:
    $>python clean —all

    and try again!
  7. Don’t try to use ./configure-make-make-install way. It crashes and probably doesn’t supported.

Good luck!