Huge surfaces - Revision history

Cchem: 1 revision

2018-04-03T18:09:01Z

1 revision

Speleo3: CA-only

2018-03-16T17:55:16Z

CA-only

Bell: 1 revision

2015-08-14T17:32:02Z

1 revision

Speleo3: atomic color

2015-07-29T15:15:58Z

atomic color

Bell: 2 revisions

2015-04-21T22:49:58Z

2 revisions

Speleo3: gaussian_b_floor

2015-02-12T22:51:43Z

gaussian_b_floor

Speleo3: gaussian_b_floor

2015-02-12T22:50:36Z

gaussian_b_floor

Pyadmin: 2 revisions

2014-03-28T01:47:07Z

2 revisions

New page

= Overview =
PyMOL can render '''very large''' (huge) surfaces of proteins, using a few tricks. First off, you should know that because of the size, you do not get the level of accuracy that you would for a smaller molecule. However, if you need to represent a molecule (or object) with a few million atoms, this may be your option of choice.

= Example =
The output from the example below is shown below. The PDB 1AON has nearly 60,000 atoms. This isn't the largest PDB, but it's a good example.

<gallery>
Image:large_surface.png
Image:large_surface_approx.png
</gallery>

= The Code =
<source lang="python">
# load a whopping big PDB
fetch 1aon, struct

# create a color spectrum over the object
spectrum count, selection=struct

# give ourselves a responsive UI
as spheres
set sphere_mode,1

# === now create a pseudo-fcalc map (a 3D volumetric scalar field) ===
# set the B-factors nice and high for smoothness
alter all, b=40

# ~10 A map resolution
set gaussian_resolution, 10

# ~10 A map spacing with a 10 A surrounding buffer
# (you may need to vary this)
map_new map, gaussian, 10, struct, 10

# create a surface from the map
isosurface surf, map, 1.0

# now color the map based on the underlying protein
ramp_new ramp, struct, [0,10,10], [-1,-1,0]

color ramp, surf

# hide the ramp
disable ramp
</source>

[[Category:Performance]]

← Older revision	Revision as of 18:09, 3 April 2018
(No difference)

@@ Line 1: / Line 1: @@
 PyMOL can render '''very large''' (huge) surfaces of proteins, using a few tricks.  First off, you should know that because of the size, you do not get the level of accuracy that you would for a smaller molecule.  However, if you need to represent a molecule (or object) with a few million atoms, this may be your option of choice.
@@ Line 10: / Line 9: @@
 </gallery>
-= The Code =
+== Strategy 1: Low resolution Gaussian Map ==
 <source lang="python">
 # load a whopping big PDB
-fetch 1aon, struct
+fetch 1aon, struct, async=0
 # create a color spectrum over the object
@@ Line 39: / Line 38: @@
 # hide the ramp
 disable ramp
 </source>
 [[Category:Performance]]

← Older revision	Revision as of 17:32, 14 August 2015
(No difference)

@@ Line 17: / Line 17: @@
 # create a color spectrum over the object
 spectrum count, selection=struct
 # === now create a pseudo-fcalc map (a 3D volumetric scalar field) ===
@@ Line 37: / Line 33: @@
 # now color the map based on the underlying protein
-ramp_new ramp, struct, [0,10,10], [-1,-1,0]
+ramp_new ramp, struct, [0,10], [atomic, atomic]
 color ramp, surf

← Older revision	Revision as of 22:49, 21 April 2015
(No difference)

@@ Line 24: / Line 24: @@
 # === now create a pseudo-fcalc map (a 3D volumetric scalar field) ===
 # set the B-factors nice and high for smoothness
-alter all, b=40
+set gaussian_b_floor, 40
 # ~10 A map resolution
 set gaussian_resolution, 10
 # ~10 A map spacing with a 10 A surrounding buffer