Cartoon: Difference between revisions

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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.


[[Image:Cartoon_ex.png|thumb|Cartoon Representation Example]]
 
[[Image:Cartoon_ex.png|thumb|center|Cartoon Representation Example|300px]]
 


===Forcing Exact Boundaries in Coloring Secondary Structures===
===Forcing Exact Boundaries in Coloring Secondary Structures===
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</code>
</code>


[[Image:Cartoon_discrete_color0.png|Discrete Coloring Off|left|thumb]] [[Image:Cartoon_discrete_color1.png|Discrete Coloring On|left|thumb]]
[[Image:Cartoon_discrete_color0.png|Discrete Coloring Off|center|thumb]] [[Image:Cartoon_discrete_color1.png|Discrete Coloring On|center|thumb]]
 


== Sausage Representation ==
== Sausage Representation ==
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==Black and White Representation==
==Black and White Representation==
For those who want a nifty black and white representation of their protein try the following:
For those who want a nifty black and white representation of their protein try the following:
* Ray trace your protein of choice in a cartoon representation use a BLACK background
# Ray trace your protein of choice in a cartoon representation use a BLACK background
* Save the image
# Save the image
* Load the image in GIMP [[Image:Bw1.jpeg|thumb|Black BG Ribbon]]
# Load the image in GIMP. [[Image:Bw1.jpeg|thumb|Black BG Ribbon|center|350px]]
* Desaturate or Grayscale the image [[Image:Bw2.jpeg|thumb|Grayscale]]
# Desaturate or Grayscale the image. [[Image:Bw2.jpeg|thumb|Grayscale|center|350px]]
* Run the filter: Filter->Edge-Detect->Edge [[Image:Bw3.jpeg|thumb|Edge Detect]]
# Run the filter: Filter->Edge-Detect->Edge. [[Image:Bw3.jpeg|thumb|Edge Detect|center|350px]]
* Select: Layers->Color->Invert [[Image:Bw4.jpeg|thumb|Invert Color]]
# Select: Layers->Color->Invert. [[Image:Bw4.jpeg|thumb|Invert Color|center|350px]]
# 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. [[Image:Bw5.jpeg|thumb|Other Styles|center|350px|Comments]]


Comments: 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. [[Image:Bw5.jpeg|thumb|Other Styles]]


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 [[:Category:Advanced_Issues_Image_Manipulation_Publication_Quatlity_Images|Creating Publication Quality Images]].

Revision as of 16:22, 16 May 2005

Cartoon Command

DESCRIPTION

"cartoon" changes the default cartoon for a set of atoms.

USAGE

  cartoon type, (selection)

  type = skip | automatic | loop | rectangle | oval | tube | arrow | dumbbell

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 strands: 

cartoon_rect_length
cartoon_rect_width

For helices: 

cartoon_oval_length
cartoon_oval_width

or for "fancy" helices: cartoon_dumbell_length cartoon_dumbell_width cartoon_dumbell_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

Black and White Representation

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.


See Also

Cmd cartoon

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