Editing Displaying Biochemical Properties (section)

==Surface-Related==

===Surface Area===
To calculate the surface area of a selection, see [[Get_Area]].

===Polar surface area===
For a solvent accessible PSA approximation:
<source lang="python">
set dot_density, 3
remove hydro
remove solvent
show dots
set dot_solvent, on
get_area elem N+O
get_area elem C+S
get_area all
</source>

For molecular PSA approximation
<source lang="python">
set dot_density, 3
remove hydro
remove solvent
set dot_solvent, off
get_area elem N+O
get_area elem C+S
get_area all
</source>

Showing dots isn't mandatory, but it's a good idea to confirm that you're getting the value for the atom dot surface you think you're using.
Please realize that the resulting numbers are only approximate, reflecting the sum of partial surface areas for all the dots you see. To increase accuracy, set dot_density to 4, but be prepared to wait...
 
===Display solvent accessible surface===
Using the surface display mode, PyMOL doesn't show the solvent accessible surface, rather it shows the solvent/protein contact surface. The solvent accessible surface area is usually defined as the surface traced out by the center of a water sphere, having a radius of about 1.4 angstroms, rolled over the protein atoms. The contact surface is the surface traced out by the vdw surfaces of the water atoms when in contact with the protein.

PyMOL can show solvent accessible surfaces using the dot or sphere representations:

for dots:
<source lang="python">
show dots
set dot_mode,1
set dot_density,3
</source>

for spheres:
<source lang="python">
alter all,vdw=vdw+1.4
show spheres
</source>

Once the Van der Waals radii for the selection have been altered, the surface representation will also be "probe-inflated" to show a pseudo solvent accessible surface, as detailed above.

for surfaces:
<source lang="python">
alter all,vdw=vdw+1.4
show surface
</source>

[[Image:solvent-accessible_surface.jpg|thumb|Solvent-Accessible Surface Example|left]]


















Note that to display both the molecular surface and the solvent-accessible surface, the object must be duplicated, as is done for [[Surface#Representation-independent Color Control]]. This also applies if the spheres representation is to be used to display "real" atoms.

===Contact Potential===
See [[Protein_contact_potential]] and [[APBS]].
[[Image:Prot_contact_pot.png|thumb|right|125px]]
<div style="clear:right;"> </div>

=== Electric Field Lines ===
[[Image:Elines.png|center|250px|thumb|PyMOL and APBS used to show electronic field lines.]]

To produce an image with electric field lines, first run APBS.  Then, input the following:
<source lang="python">
gradient my_grad, pymol-generated
ramp_new my_grad_ramp, pymol-generated
color my_grad_ramp, my_grad
</source>

===Residues with functional groups===
[[Image:1igt_cys_lys_asp_glu_colored.png|thumb|200px|Whole residues colored (Cys: yellow, Lys: blue, Asp and Glu: red)]]
Poor man's solution: Display protein as surface, colorize all Lys (-NH2), Asp and Glu (-COOH) and Cys (-SH):
<source lang="python">
remove resn hoh    # remove water
h_add              # add hydrogens

as surface
color grey90

color slate, resn lys       # lysines in light blue
color paleyellow, resn cys  # cysteines in light yellow
color tv_red, (resn asp or(resn glu))  # aspartic and glutamic acid in light red
</source>

[[Image:1igt_functional_groups_colored.png|thumb|200px|Only central atoms of functional groups colored (Cys: S, Lys: NH2, Asp and Glu: CO2)]]
Not-''so''-poor-man's solution: In order to have the functional groups better localized, only the central atoms can be colored: 
* the S atom of cystein, 
* the N and H atoms of the free amine of lysine (may be displayed with three H atoms at all three possible positions)
* the C and two O atoms of free carboxylic groups in aspartic and glutamic acid 
In this way, they are better visible through the surface compared to only one colored atom, both amines and carboxylic groups consist of three colored atoms each.
<source lang="python">
remove resn hoh    # remove water
h_add              # add hydrogens

as surface
color grey90

select sulf_cys, (resn cys and (elem S))      # get the sulfur atom of cystein residues
color yellow, sulf_cys

select nitro_lys, (resn lys and name NZ)              # get the nitrogens of free amines ("NZ" in PDB file)
select hydro_lys, (elem H and (neighbor nitro_lys))   # get the neighboring H atoms 
select amine_lys, (nitro_lys or hydro_lys)
color tv_blue, amine_lys


select oxy_asp, (resn asp and (name OD1 or name OD2))             # get the two oxygens of -COOH  ("OD1", "OD2")
select carb_asp, (resn asp and (elem C and (neighbor oxy_asp)))   # get the connecting C atom
select oxy_glu, (resn glu and (name OE1 or name OE2))             # oxygens "OE1" and "OE2" in PDB file
select carb_glu, (resn glu and (elem c and (neighbor oxy_glu)))
select carboxy, (carb_asp or oxy_asp or carb_glu or oxy_glu)
color tv_red, carboxy
</source>

By displaying the protein as non-transparent surface, only the functional groups (colored atoms) at the surface are visible. The visualization of those groups can be pronounced by displaying the corresponding atoms as spheres, e.g. "as spheres, carboxy + amine_lys + sulf_cys", in this way it might become more clear how accessible they are.

When displaying the protein as cartoon, the functional groups can be shown as spheres, and the whole residues cys, lys, asp and glu as sticks connected to the backbone, with the atoms of the functional groups again as spheres. However, then also the not accessible residues inside the protein are visible.