Surface

2007-06-25T17:29:33Z

Talbotron22: changed teh -> the

The surface representation of a protein, in PyMol, shows the "Connolly" surface or the surface that would be traced out by the '''surfaces''' of waters in contact with the protein at all possible positions. [[Image:Surface_ex.png|thumb|Surface Representation Example|right]]

==Enabling==
To enable the surface representation do
show surface, SEL
for any proper selection SEL.

==Settings==
===Transparency===
To adjust the transparency of surfaces try:
<source lang="python">
set transparency, 0.5
</source>
Where 1.0 will be an invisible and 0.0 a completely solid surface.

===Quality===
To smooth your surface representation try:
<source lang="python">
set surface_quality, 1
</source>
or higher if you wish, though it will take longer and might look odd.

===Probe Radius===
To change the probe radius other than default 1.4 Å, you need to change the solvent radius, say, 1.6 Å:
<source lang="python">
set solvent_radius, 1.6
</source>
If the surface does not change correspondingly, use:
<source lang="python">
rebuild
</source>

==Tips==
===Displaying a protein as surface with a ligand as sticks===
The easiest way to do this is to create separate objects for each type of display.

- Load your protein
- Select the ligand
- Create a separate object for the ligand
- Remove ligand atoms from the protein
- Display both objects separately

Example:
<source lang="python">
load prot.ent,protein
select ligand,resn FAD
create lig_sticks,ligand
remove ligand
show sticks,lig_sticks
show surface,protein
</source>

===Calculating a partial surface===
There is, until now, an undocumented way to calculate a surface for only a part of an object without creating a new one:
<source lang="python">
flag ignore, not A/49-63/, set
delete indicate
show surface
</source>
If the surface was already computed, then you'll also need to issue the command:
<source lang="python">
rebuild
</source>

===Displaying surface inside a molecule===
As far as I can tell, setting ambient to zero alone doesn't quite do the job, since some triangles still get lit by the light source. The best combination I can find is:
<source lang="python">
set ambient=0
set direct=0.7
set reflect=0.0
set backface_cull=0
</source>
Which gives no shadows and only a few artifacts.

As an alternative, you might just consider showing the inside of the surface directly...that will create less visual artifacts, and so long as ambient and direct are sufficiently low, it will look reasonable in "ray".
<source lang="python">
util.ray_shadows("heavy")
set two_sided_lighting=1
set backface_cull=0
</source>

===Creating a Closed Surface===
[[Image:Surface_open.png|thumb|Example OPEN Surface|left|200px]]
[[Image:Surface_closed.png|thumb|Example CLOSED Surface|left|200px]]

To create what I'll call a '''closed surface''' (see images), you need to first make your atom selections, then create a new object for that selection then show the surface for that object. Here's an example.

sel A, id 1-100
create B, A
show surface, B

[[Category:Representations|Surface]]

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Surface