Editing Surface (section)

==Tips==

=== Exporting Surface/Mesh Coordinates to File===

PyMOL can export its coordinates as WRL wireframe model files for VRML input.

====Older PyMOL Versions====
<source lang="python">
# export the coordinates to povray
open("surface.inc","w").write(cmd.get_povray()[1])
</source>

====Newer PyMOL Versions====
<source lang="python">
# export the coordinates to .wrl file
save myscene.wrl
</source>
or
<source lang="python">
# export the coordinates to .obj file. Only surface representation can be saved as .obj.
# NOTE: the coordinates are saved in camera coordinate system.
save myscene.obj
</source>

===Representation-independent Color Control===
To color the surface representation a different color than the underlying cartoon or ligand representations, simply duplicate the object, show only the surface in the duplicate, and show only the cartoon and/or ligands in the original object.

Or use the [[surface_color]] setting that is available.



[[Image:Representation independent color control.jpg|thumb|Representation-independent Color Control Example|left]]

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

1 Load your protein

2 Select the ligand 

3 Create a separate object for the ligand 

4 Remove ligand atoms from the protein

5 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>


Even easier is to:

1 Load the protein

2 S (Show) > organic > stick

3 S (Show) > surface

===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>

See [[Get_Area]] for more information on surface area calculations.

===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===
<gallery>
Image:Surface_open.png|Example OPEN Surface
Image:Surface_closed.png|Example CLOSED Surface
</gallery>

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.
<source lang="python">
 sel A, id 1-100
 create B, A
 show surface, B
</source>

===Smooth surface quick (blob)===
To get a quick blob type surface (not as accurate):
<source lang="python">
set solvent_radius, 4   
alter all, vdw=4 
sort
set surface_quality, 1
</source>

===Smooth surface accurate (blob)===
To get an accurate blob type surface:
<source lang="python">
set surface_quality, 1
alter all, b=50
alter all, q=1
set gaussian_resolution,5
map_new mapA, gaussian, 1, sele or pdb, 6
isosurface surfA, mapA
</source>
'''Notes:''' Set gaussian resolution is variable with a larger number causing a more smooth surface (4 is medium and 8 is very smooth).
The temperature factor field (b) has at least as much impact as the resolution setting, so increasing b factors is the more computationally efficient way of increasing the blur effect.
If you are displaying more then one surface in a .pse file you must create a new map for each one (if you have three you will create mapA for the first, mapB for the second and mapC for the third), then you apply an isosurface to each map (isosurface surfA, mapA - isosurface surfB, mapB - isosurface surfC, mapC).

=== Huge Surfaces ===
If your protein or complex is too large to render ([[ray]] runs out of RAM, for example) then check out the [[Huge_surfaces|tip for huge surfaces]].