#############################################################
# Cameron Mura, March 2002
#
# PyMOL script file to make 2 .png figures of the electron 
# density surrounding Ser99 in chain B: first file is 2Fo-Fc
# density [using model-derived phases] and second file is 
# Fobs density [using observed amplitudes and experimental 
# phases (from SeMet MAD phasing)].
#############################################################

# Set background color to white:

bg_color white

# Set parameters to make electron density meshes real purty,
# and stick radius for protein molecule:

set mesh_radius = 0.018
set antialias = 1
set stick_radius = 0.12

# Load PDB and XPLOR-formatted map files:

load PaeSurE_fordensity.pdb.txt, sure
load map2fofc_nonds.xplor, 2fofc
load dm_phex20_ncs.xplor, phex

# Show e-density maps centered on residue Ser99 in chain B.
# They will be called "mesh1" and "mesh2" and both will be 
# contoured at +1.4-sigma. Show all density within a border 
# of 5.0 Angstroms.

isomesh mesh1, 2fofc, 1.4, (resid 99 and chain B), 5
isomesh mesh2, phex, 1.4, (resid 99 and chain B), 5

# Show molecule in stick format & color various objects:
# Carbon atoms = grey; 2Fo-Fc density (mesh1) = blue;
# Fobs,MAD density (mesh2) = green

show sticks, sure
hide lines, sure
color grey, (sure and element c)
color blue, mesh1
color forest, mesh2

# Initial zoom-in on Ser99 in chain B and clip the slab for a clearer view.
# [ NOTE: actually don't want to "zoom" because (for some reason that I don't
#   understand at first glance) it ruins the orientation set by the 'set_view'
#   command in the next section. ]
#zoom (resid 99 and chain B)

set_view (\
    -0.863467157,   -0.272126764,   -0.424702108,\
    -0.428088963,   -0.049945842,    0.902353704,\
    -0.266766369,    0.960965395,   -0.073367499,\
     0.000000000,    0.000000000,  -22.312648773,\
    -3.462500095,   58.056999207,   29.152500153,\
    20.520223618,   31.020223618,    0.000000000 )
### cut above here and paste into script ###

clip slab, 11.0

# Show mesh1, hide mesh2, do ray-tracing, and write out the graphics file:
hide mesh, mesh2
show mesh, mesh1
ray 800,600
png PaeSurE_2fofc_Ser99.png

# Now do the same for mesh2, hiding mesh1, etc...
hide mesh, mesh1
show mesh, mesh2
ray 800,600
png PaeSurE_Fobs_Ser99.png

# Quit PyMOL:
quit