Viewing Electron Density in PyMOL - [ Ссылка ]

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00:00:21 Introduction
00:02:30 GUI
00:07:35 Command line

Useful links
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#########################
00:02:30 Electron density in the GUI
rein

# load molecule
fetch 2F67

# clean and present
remove solvent + inorganic
util.cbc
as sticks
bg_color white
util.cnc
orient

#### bring in the density map
# density map
fetch 2F67, type=2fofc

# map object has been created!
# lets create a contour mesh
2F67_2fofc : [A] : mesh : @ level 1.0
2F67_2fofc_mesh : [C] : blue
2F67_2fofc_mesh : [A] : rename # suffix with '1'

# lets create a second contour mesh
2F67_2fofc : [A] : mesh : @ level 2.0
2F67_2fofc_mesh : [C] : magenta
2F67_2fofc_mesh : [A] : rename # suffix with '2'

# take a picture?
as sticks
set mesh_width, 0.5


#########################
00:07:35 Electron density on the command line
rein

# load molecule
fetch 2F67

# clean and present
remove solvent + inorganic
util.cbc
as sticks
bg_color white
util.cnc
orient

#### bring in the density map
# density map
fetch 2F67, type=2fofc

# difference map
fetch 2F67, type=fofc

# density map parameters
isomesh 2F67-2fofc-den, 2F67_2fofc, 1.5
color blue, 2F67-2fofc-den

# difference map parameters
isomesh 2F67-fofc-pos, 2F67_fofc, 3
isomesh 2F67-fofc-neg, 2F67_fofc, -3
color green, 2F67-fofc-pos
color red, 2F67-fofc-neg

# trim the map around structures
select chaina, c. A
isomesh mesh_cA_carved, 2F67_2fofc, 1.5, selection=(chaina), carve=2
color blue, mesh_cA_carved

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