Difference between revisions of "Cartoon"

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(Other Nucleic Acids & Cartoon Settings)
(numeric values)
 
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===USAGE===
 
===USAGE===
 +
<source lang="python">
 
  cartoon type, (selection)
 
  cartoon type, (selection)
+
</source>
type = skip | automatic | loop | rectangle | oval | tube | arrow | dumbbell
+
 
 +
'''type:'''
 +
* skip (-1)
 +
* automatic (0) (use [[dss|ss]] property)
 +
* loop (1)
 +
* rectangle (2)
 +
* oval (3)
 +
* tube (4)
 +
* arrow (5)
 +
* dumbbell (6) (see also [[cartoon_fancy_helices]])
 +
* putty (7) (b-factor scaling)
 +
* dash (8) ''(new in PyMOL 1.8.2)''
 +
 
 +
<gallery widths="200px" heights="200px">
 +
Image:Cartoon_skip.png|cartoon_skip; yes, blank.
 +
Image:Cartoon_automatic.png|cartoon_automatic
 +
Image:Cartoon_loop.png|cartoon_loop
 +
Image:Cartoon_rectangle.png|cartoon_rectangle
 +
Image:Cartoon_oval.png|cartoon_oval
 +
Image:Cartoon_tube.png|cartoon_tube
 +
Image:Cartoon_arrow.png|cartoon_arrow
 +
Image:Cartoon_dumbbell.png|cartoon_dumbbell
 +
</gallery>
  
 
===PYMOL API===
 
===PYMOL API===
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<source lang="python">
 
<source lang="python">
 
cartoon_loop_radius
 
cartoon_loop_radius
 +
</source>
 +
 +
For nucleic acid backbones which resemble 'loops'; however, are not classified as such by PyMOL (see more about nucleic acid representation settings at bottom of page):
 +
<source lang="python">
 +
cartoon_tube_radius,0.8
 
</source>
 
</source>
  
 
For "fancy" &alpha;-helices:
 
For "fancy" &alpha;-helices:
 
<source lang="python">
 
<source lang="python">
cartoon_dumbell_length
+
cartoon_dumbbell_length
cartoon_dumbell_width
+
cartoon_dumbbell_width
cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon)
+
cartoon_dumbbell_radius (radius of cylinder at edge of helix ribbon)
 
</source>
 
</source>
 +
  
 
In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.
 
In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.
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===Forcing Exact Boundaries in Coloring Secondary Structures===
 
===Forcing Exact Boundaries in Coloring Secondary Structures===
To force PyMol to respect secondary structural elements color-wise (PyMol smooths out colors near color chagnes for a prettier image) use the following  
+
To force PyMOL to respect secondary structural elements color-wise (PyMOL smooths out colors near color chagnes for a prettier image) use the following  
PyMol command:
+
PyMOL command:
 
<code>
 
<code>
 
set cartoon_discrete_colors, on
 
set cartoon_discrete_colors, on
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== Sausage Representation ==
 
== Sausage Representation ==
The familiar sausage representation in PyMol is called, "putty".  To enable the putty/sausage view simply do,
+
The familiar sausage representation in PyMOL is called, "putty".  To enable the putty/sausage view simply do,
 
  show cartoon
 
  show cartoon
 
  cartoon putty
 
  cartoon putty
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I'm sure there are other ways to do this.  If you want to include it in a publication make sure you ray traced it large enough.  For that, see [[:Category:Advanced_Issues_Image_Manipulation_Publication_Quatlity_Images|Creating Publication Quality Images]].
+
I'm sure there are other ways to do this.  If you want to include it in a publication make sure you ray traced it large enough.  For that, see [[Publication_Quality_Images|Creating Publication Quality Images]].
  
 
==CA (Alpha Carbon) Trace==
 
==CA (Alpha Carbon) Trace==
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==Various Transparency Levels==
 
==Various Transparency Levels==
 
[[Image:Cartoon_multi_transp.png|thumb|center|Example of Cartoon Multi-level Transparency.  The near cartoon has transparency setting '''0.2''', the segment in the BG '''0.5'''.]]
 
[[Image:Cartoon_multi_transp.png|thumb|center|Example of Cartoon Multi-level Transparency.  The near cartoon has transparency setting '''0.2''', the segment in the BG '''0.5'''.]]
One can make different cartoon selections have different transparency values, in PyMol.  The trick here is to use "create" instead of "select".  Create makes new objects that can have independent settings.
+
One can make different cartoon selections have different transparency values, in PyMOL.  The trick here is to use "create" or "extract" instead of "select".  Create makes new objects that can have independent settings while leaving the original object intact, whereas extract removes the specified atoms from the original object when creating the new object.
  
 
<source lang="python">
 
<source lang="python">
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# transfer a piece of the molecule into a new object
 
# transfer a piece of the molecule into a new object
 
+
extract new_obj, chain A
create new_obj, chain A
 
remove mol_obj in new_obj
 
  
 
# adjust trasparency for the new object
 
# adjust trasparency for the new object
 
 
set cartoon_transparency, 0.5, new_obj
 
set cartoon_transparency, 0.5, new_obj
 
</source>
 
</source>
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== Nucleic Acid Representation ==
 
== Nucleic Acid Representation ==
 
[[Image:Nucleic1.png|thumb|center|Showing Nucleic Acids]]
 
[[Image:Nucleic1.png|thumb|center|Showing Nucleic Acids]]
 +
To control radius of nucleic acids default backbone cartoon:
 +
<source lang="python">
 +
set cartoon_tube_radius,0.8  #0.5 seems close to the default setting
 +
</source>
 +
 
To show nucleic acids in a nicer format do:
 
To show nucleic acids in a nicer format do:
 
<source lang="python">
 
<source lang="python">
Line 119: Line 150:
 
  show cartoon
 
  show cartoon
 
</source>
 
</source>
 +
 +
  
 
=== Other Nucleic Acids & Cartoon Settings ===
 
=== Other Nucleic Acids & Cartoon Settings ===
Line 149: Line 182:
  
 
[[Examples of nucleic acid cartoons]]
 
[[Examples of nucleic acid cartoons]]
 +
 +
== Breaking Up a Visualization with Cartoon Skip ==
 +
<source lang="python">
 +
fetch 1cll, async=0
 +
 +
create a_copy, 1cll
 +
 +
# show them as cartoons
 +
 +
color blue, 1cll
 +
 +
set cartoon_highlight_color, green, 1cll
 +
 +
color marine, a_copy
 +
 +
set cartoon_highlight_color, magenta, a_copy
 +
 +
# select the region of interest
 +
 +
select to_hide, i. 0-79
 +
 +
show_as cartoon
 +
 +
cartoon skip, to_hide and 1cll
 +
 +
orient
 +
 +
# hide/skip this section in the original
 +
 +
cartoon skip, i. 81-200 and a_copy
 +
 +
ray
 +
 +
</source>
 +
  
 
== See Also ==
 
== See Also ==
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[[Category:Representations|Cartoon]]
 
[[Category:Representations|Cartoon]]
 
[[Category:Nucleic_Acids|Cartoon]]
 
[[Category:Nucleic_Acids|Cartoon]]
 +
[[Category:Putty]]

Latest revision as of 12:55, 17 December 2017

Cartoon Command

DESCRIPTION

cartoon changes the default cartoon for a set of atoms.

USAGE

 cartoon type, (selection)

type:

  • skip (-1)
  • automatic (0) (use ss property)
  • loop (1)
  • rectangle (2)
  • oval (3)
  • tube (4)
  • arrow (5)
  • dumbbell (6) (see also cartoon_fancy_helices)
  • putty (7) (b-factor scaling)
  • dash (8) (new in PyMOL 1.8.2)

PYMOL API

cmd.cartoon(string type, string selection )

EXAMPLES

cartoon rectangle,(chain A)
cartoon skip,(resi 145:156)

NOTES

the "automatic" mode utilizes ribbons according to the information in the PDB HELIX and SHEET records.

Adjusting width of cartoon

Try varying the following.

For β-strands:

cartoon_rect_length
cartoon_rect_width

For α-helices:

cartoon_oval_length
cartoon_oval_width

For loops:

cartoon_loop_radius

For nucleic acid backbones which resemble 'loops'; however, are not classified as such by PyMOL (see more about nucleic acid representation settings at bottom of page):

cartoon_tube_radius,0.8

For "fancy" α-helices:

cartoon_dumbbell_length
cartoon_dumbbell_width
cartoon_dumbbell_radius  (radius of cylinder at edge of helix ribbon)


In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.


Cartoon Representation Example


Forcing Exact Boundaries in Coloring Secondary Structures

To force PyMOL to respect secondary structural elements color-wise (PyMOL smooths out colors near color chagnes for a prettier image) use the following PyMOL command: set cartoon_discrete_colors, on

Discrete Coloring Off
Discrete Coloring On

Sausage Representation

The familiar sausage representation in PyMOL is called, "putty". To enable the putty/sausage view simply do,

show cartoon
cartoon putty
unset cartoon_smooth_loops
unset cartoon_flat_sheets

As of v 0.98 or so, there's a Putty option. Use this.

Example of B-factor Putty

Black and White Representation

UPDATE: This method is essentially obseleted by the new setting set ray_trace_mode,2. More information on this at Ray. For those who want a nifty black and white representation of their protein try the following:

  1. Ray trace your protein of choice in a cartoon representation use a BLACK background
  2. Save the image
  3. Load the image in GIMP.
    Black BG Ribbon
  4. Desaturate or Grayscale the image.
    Grayscale
  5. Run the filter: Filter->Edge-Detect->Edge.
    Edge Detect
  6. Select: Layers->Color->Invert.
    Invert Color
  7. Different methods of edge detection will give you different results. In the last example, I used Laplace Edge-Detect, then painted an all white layer beneath the current layer to achieve the results.
    Comments


I'm sure there are other ways to do this. If you want to include it in a publication make sure you ray traced it large enough. For that, see Creating Publication Quality Images.

CA (Alpha Carbon) Trace

If you have a structure with just a alpha carbon trace, you can get a cartoon by

set cartoon_trace,1
show cartoon

If your structure is more than just the CA backbone, the cartoon representation will look incorrect, so use it just with CA trace.

Various Transparency Levels

Example of Cartoon Multi-level Transparency. The near cartoon has transparency setting 0.2, the segment in the BG 0.5.

One can make different cartoon selections have different transparency values, in PyMOL. The trick here is to use "create" or "extract" instead of "select". Create makes new objects that can have independent settings while leaving the original object intact, whereas extract removes the specified atoms from the original object when creating the new object.

load mol_obj.pdb

# transfer a piece of the molecule into a new object
extract new_obj, chain A

# adjust trasparency for the new object
set cartoon_transparency, 0.5, new_obj

Nucleic Acid Representation

Showing Nucleic Acids

To control radius of nucleic acids default backbone cartoon:

set cartoon_tube_radius,0.8   #0.5 seems close to the default setting

To show nucleic acids in a nicer format do:

 set cartoon_ring_mode,1
 show cartoon


Other Nucleic Acids & Cartoon Settings

Here are some things to try:

set cartoon_ring_mode, 1   # (or 2 or 3)
set cartoon_ring_finder, 1 # (or 2 or 3 or 4)
set cartoon_nucleic_acid_mode, 0   # (or 1 or 2 or 3 or 4)

set cartoon_side_chain_helper
rebuild

set cartoon_ring_transparency, 0.5

set cartoon_ladder_mode, 0 # or 1

set cartoon_ladder_color, color-name
set cartoon_nucleic_acid_color, color-name

cartoon oval
set cartoon_oval_width, 0.8

cartoon rect

cartoon dumbbell
set cartoon_dumbbell_width, 0.4
set cartoon_dumbbell_radius, 0.4

Overview of nucleic acid cartoons

Examples of nucleic acid cartoons

Breaking Up a Visualization with Cartoon Skip

fetch 1cll, async=0

create a_copy, 1cll

# show them as cartoons

color blue, 1cll

set cartoon_highlight_color, green, 1cll

color marine, a_copy

set cartoon_highlight_color, magenta, a_copy

# select the region of interest

select to_hide, i. 0-79

show_as cartoon

cartoon skip, to_hide and 1cll

orient

# hide/skip this section in the original

cartoon skip, i. 81-200 and a_copy

ray


See Also

Displaying_Biochemical_Properties