Cartoon - Revision history

Cchem: 1 revision

2018-01-08T04:03:20Z

1 revision

Speleo3: numeric values

2017-12-17T16:55:24Z

numeric values

Cchem: 1 revision

2016-05-01T04:43:45Z

1 revision

Speleo3: dash

2016-04-11T22:06:30Z

dash

Cchem: 2 revisions

2016-04-04T00:22:28Z

2 revisions

Jaredsampson: /* Various Transparency Levels */ include mention of "extract"

2016-03-28T05:44:38Z

Various Transparency Levels: include mention of "extract"

Cchem at 07:09, 27 March 2016

2016-03-27T07:09:12Z

Pyadmin: 16 revisions

2014-03-28T01:42:54Z

16 revisions

New page

==Cartoon Command==
===DESCRIPTION===
'''cartoon''' changes the default cartoon for a set of atoms.

===USAGE===
<source lang="python">
cartoon type, (selection)
</source>

'''type:'''
#skip
#automatic
#loop
#rectangle
#oval
#tube
#arrow
#dumbbell

<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===
<source lang="python">
cmd.cartoon(string type, string selection )
</source>

===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:
<source lang="python">
cartoon_rect_length
cartoon_rect_width
</source>

For α-helices:
<source lang="python">
cartoon_oval_length
cartoon_oval_width
</source>

For loops:
<source lang="python">
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>

For "fancy" α-helices:
<source lang="python">
cartoon_dumbbell_length
cartoon_dumbbell_width
cartoon_dumbbell_radius (radius of cylinder at edge of helix ribbon)
</source>

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|center|Cartoon Representation Example|300px]]

===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:
<code>
set cartoon_discrete_colors, on
</code>

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

== 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.

[[Image:B_factor_putty.png|thumb|Example of B-factor Putty|center|250px]]

==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:
# Ray trace your protein of choice in a cartoon representation use a BLACK background
# Save the image
# Load the image in GIMP. [[Image:Bw1.jpeg|thumb|Black BG Ribbon|center|350px]]
# 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|center|350px]]
# 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]]

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==
If you have a structure with just a alpha carbon trace, you can get a cartoon by
<source lang="python">
set cartoon_trace,1
show cartoon
</source>
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==
[[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.

<source lang="python">
load mol_obj.pdb

# transfer a piece of the molecule into a new object

create new_obj, chain A
remove mol_obj in new_obj

# adjust trasparency for the new object

set cartoon_transparency, 0.5, new_obj
</source>

== Nucleic Acid Representation ==
[[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:
<source lang="python">
set cartoon_ring_mode,1
show cartoon
</source>

=== Other Nucleic Acids & Cartoon Settings ===
Here are some things to try:
<source lang="python">
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
</source>
[[Overview 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 ==
[[Displaying_Biochemical_Properties]]

[[Category:Representations|Cartoon]]
[[Category:Nucleic_Acids|Cartoon]]
[[Category:Putty]]

SavinaRoja: /* Adjusting width of cartoon */

2010-12-08T05:06:07Z

Adjusting width of cartoon

Karo: link repaired

2010-09-21T11:08:02Z

link repaired

New page

==Cartoon Command==
===DESCRIPTION===
'''cartoon''' changes the default cartoon for a set of atoms.

===USAGE===
<source lang="python">
cartoon type, (selection)
</source>

'''type:'''
#skip
#automatic
#loop
#rectangle
#oval
#tube
#arrow
#dumbbell

<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===
<source lang="python">
cmd.cartoon(string type, string selection )
</source>

===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:
<source lang="python">
cartoon_rect_length
cartoon_rect_width
</source>

For α-helices:
<source lang="python">
cartoon_oval_length
cartoon_oval_width
</source>

For loops:
<source lang="python">
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>

For "fancy" α-helices:
<source lang="python">
cartoon_dumbell_length
cartoon_dumbell_width
cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon)
</source>

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|center|Cartoon Representation Example|300px]]

===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:
<code>
set cartoon_discrete_colors, on
</code>

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

== 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.

[[Image:B_factor_putty.png|thumb|Example of B-factor Putty|center|250px]]

==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:
# Ray trace your protein of choice in a cartoon representation use a BLACK background
# Save the image
# Load the image in GIMP. [[Image:Bw1.jpeg|thumb|Black BG Ribbon|center|350px]]
# 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|center|350px]]
# 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]]

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==
If you have a structure with just a alpha carbon trace, you can get a cartoon by
<source lang="python">
set cartoon_trace,1
show cartoon
</source>
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==
[[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.

<source lang="python">
load mol_obj.pdb

# transfer a piece of the molecule into a new object

create new_obj, chain A
remove mol_obj in new_obj

# adjust trasparency for the new object

set cartoon_transparency, 0.5, new_obj
</source>

== Nucleic Acid Representation ==
[[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:
<source lang="python">
set cartoon_ring_mode,1
show cartoon
</source>

=== Other Nucleic Acids & Cartoon Settings ===
Here are some things to try:
<source lang="python">
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
</source>
[[Overview of nucleic acid cartoons]]

[[Examples of nucleic acid cartoons]]

== See Also ==
[[Displaying_Biochemical_Properties]]

[[Category:Representations|Cartoon]]
[[Category:Nucleic_Acids|Cartoon]]
[[Category:Putty]]

@@ Line 9: / Line 9: @@
 '''type:'''
-#skip
+* skip (-1)
-#automatic
+* automatic (0) (use [[dss|ss]] property)
-#loop
+* loop (1)
-#rectangle
+* rectangle (2)
-#oval
+* oval (3)
-#tube
+* tube (4)
-#arrow
+* arrow (5)
-#dumbbell
+* dumbbell (6) (see also [[cartoon_fancy_helices]])
-#dash ''(new in PyMOL 1.8.2)''
+* putty (7) (b-factor scaling)
 <gallery widths="200px" heights="200px">

← Older revision	Revision as of 04:03, 8 January 2018
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← Older revision	Revision as of 04:43, 1 May 2016
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← Older revision	Revision as of 00:22, 4 April 2016
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@@ Line 124: / Line 124: @@
 ==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'''.]]
-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">
@@ Line 130: / Line 130: @@
 # 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
 </source>

@@ Line 61: / Line 61: @@
 </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):
+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
@@ Line 81: / Line 81: @@
 ===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>
 set cartoon_discrete_colors, on
@@ Line 90: / Line 90: @@
 == 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
   cartoon putty
@@ Line 124: / Line 124: @@
 ==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'''.]]
-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" instead of "select".  Create makes new objects that can have independent settings.
 <source lang="python">

@@ Line 68: / Line 68: @@
 For "fancy" &alpha;-helices:
 <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>