Difference between revisions of "Examples of nucleic acid cartoons"

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== pymol version info ==
+
== Default settings ==
−
The various new nucleic acid display settings for PyMol 0.99 listed below were produced using version 0.99 beta 29 on Windows XP with an arbitrary B-form DNA molecule. Higher values could be set for each setting but appeared to yield the default representations.
 
−
== default settings ==
 
 
The defaults give a phosphate backbone with single sticks passing across the full width of the base plane.
 
The defaults give a phosphate backbone with single sticks passing across the full width of the base plane.
 
<source lang="python">
 
<source lang="python">
−
set cartoon_nucleic_acid_mode, 1 # backbone follows phosphates
+
set cartoon_nucleic_acid_mode, 0 # backbone follows phosphates; actually Pymol itself uses setting '4' as default
 
set cartoon_ladder_mode, 1 # sticks from backbone into nucleotide
 
set cartoon_ladder_mode, 1 # sticks from backbone into nucleotide
 
set cartoon_ring_mode, 0 # no nucleotide rings
 
set cartoon_ring_mode, 0 # no nucleotide rings
−
set cartoon_ring_finder, 1 # ribose and base rings (not displayed as ring mode 0)
+
set cartoon_ring_finder, 1 # ribose and base rings (not displayed since ring mode 0)
 
</source>
 
</source>
 
{|
 
{|
−
|[[Image:DNAcartoon_ringmode0_laddermode1_ringfinder1_nucleicacidmode0.png|default view|thumb]]
+
|[[Image:DNA-default-ring0-ladder1-na0-finder1.png|default view|thumb]]
 
|}
 
|}
−
== cartoon ring modes ==
+
<!-- Prior to 4-15-09 cartoon_nucleic_acid_mode had been listed as being default value of 1 but this would go through C3, right? Fixed so value listed for cartoon_nucleic_acid_mode is 4 which is for following phosphates and colors the same when I look at RNA ends of 1e7k. None of the other settings looked as same as it did when opening Pymol. Any other settings don't look like the default I see when opening Pymol for RNA in 1e7k. -->
−
<source lang="python">
+
 
−
set cartoon_ring_mode, 0 # no nucleotide rings
+
== Cartoon ring mode ==
−
set cartoon_ring_mode, 1 # filled rings extending to outside edge of bonds
+
 
−
set cartoon_ring_mode, 2 # filled rings extending to inside edge of bonds
+
=== Settings ===
−
set cartoon_ring_mode, 3 # filled rings with bonds as thicker lines
+
 
−
</source>
+
<pre>set cartoon_ring_mode, value</pre>
 +
{|}
 +
!value !!align="left"|  effect
 +
|-
 +
|align="center" | 0 || stick from backbone atom to N1 of purines and N3 of pyrimidines
 +
|-
 +
|align="center" | 1 || simple plane for ribose and base rings covering area between ring bonds
 +
|-
 +
|align="center" | 2 || simple plane for ribose and base rings covering area inside sticks (slightly smaller than mode 1)
 +
|-
 +
|align="center" | 3 || plane bounded by sticks for ribose and base rings
 +
|-
 +
|align="center" | 4 || large sphere of ring diameter at centre of ribose and each base ring
 +
|-
 +
|align="center" | 5 || small sphere of 1/10 diameter at centre of ribose and each base ring
 +
|}
 +
 
 +
=== Examples ===
 +
 
 
{|
 
{|
−
|[[Image:DNAcartoon_ringmode0_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,0|thumb]]
+
|[[Image:DNA-ring0-ladder1-na0-finder1.png|cartoon_ring_mode,0|thumb]]
−
|[[Image:DNAcartoon_ringmode1_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,1|thumb]]
+
|[[Image:DNA-ring1-ladder1-na0-finder1.png|cartoon_ring_mode,1|thumb]]
−
|[[Image:DNAcartoon_ringmode2_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,2|thumb]]
+
|[[Image:DNA-ring2-ladder1-na0-finder1.png|cartoon_ring_mode,2|thumb]]
−
|[[Image:DNAcartoon_ringmode3_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,3|thumb]]
+
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ring_mode,3|thumb]]
 +
|[[Image:DNA-ring4-ladder1-na0-finder1.png|cartoon_ring_mode,4|thumb]]
 +
|[[Image:DNA-ring5-ladder1-na0-finder1.png|cartoon_ring_mode,5|thumb]]
 
|}
 
|}
 
<center>all with defaults:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i></center>
 
<center>all with defaults:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i></center>
−
== cartoon ladder modes ==
+
 
−
<source lang="python">
+
== Cartoon ring finder ==
−
set cartoon_ladder_mode, 0 # no ladder
+
 
−
set cartoon_ladder_mode, 1 # with ladder, as stick (if ring mode 0) or link to ring (if rings)
+
=== Settings ===
−
</source>
+
<pre>set cartoon_ring_finder, value</pre>
−
note that the visibility of the ladder sticks depends on ring mode >0, ring finder >0, nucleic acid mode  = 0
+
{|
 +
!value !! align="left" | effect
 +
|-
 +
|align="center" | 0 || no rings or sticks joining them
 +
|-
 +
|align="center" | 1 || both ribose and base ring
 +
|-
 +
|align="center" | 2 || only base ring(s), stick connects directly from phosphate to ring
 +
|-
 +
|align="center" | 3 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?
 +
|-
 +
|align="center" | 4 || very similar to ring finder 1:  finds ribose and base of nucleotides, and aromatic side chains of proteins
 +
|-
 +
|align="center" | 5 || sticks visible but rings invisible
 +
|}
 +
 
 +
=== Examples ===
 +
 
 +
{|
 +
|[[Image:DNA-ring3-ladder1-na0-finder0.png|cartoon_ring_finder,0|thumb]]
 +
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ring_finder,1|thumb]]
 +
|[[Image:DNA-ring3-ladder1-na0-finder2.png|cartoon_ring_finder,2|thumb]]
 +
|[[Image:DNA-ring3-ladder1-na0-finder3.png|cartoon_ring_finder,3|thumb]]
 +
|[[Image:DNA-ring3-ladder1-na0-finder4.png|cartoon_ring_finder,4|thumb]]
 +
|[[Image:DNA-ring3-ladder1-na0-finder5.png|cartoon_ring_finder,5|thumb]]
 +
|}
 +
all with:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0</i>
 +
 
 +
== Cartoon ladder mode ==
 +
 
 +
=== Settings ===
 +
 
 +
<pre>set cartoon_ladder_mode, value</pre>
 +
{|
 +
!value !! align="left" | effect
 +
|-
 +
|align="center" | 0 || no sticks shown
 +
|-
 +
|align="center" | 1 || sticks show
 +
|}
 +
 
 +
=== Examples ===
 +
 
 
{|
 
{|
−
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode0.png|cartoon_ladder_mode,0|thumb]]
+
|[[Image:DNA-ring3-ladder0-na0-finder1.png|cartoon_ladder_mode,0|thumb]]
−
|[[Image:DNAcartoon_ringfinder3_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ladder_mode,1|thumb]]
+
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ladder_mode,1|thumb]]
 
|}
 
|}
 
all with:&nbsp;<i>cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i>
 
all with:&nbsp;<i>cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i>
−
== cartoon nucleic acid modes ==
+
 
−
<source lang="python">
+
Note that the visibility of the ladder sticks depends on ring mode >0, ring finder >0, nucleic acid mode  = 0
−
set cartoon_nucleic_acid_mode, 0 # backbone follow phosphates (red)
+
 
−
set cartoon_nucleic_acid_mode, 1 # backbone follows C4' of ribose (green)
+
== Cartoon nucleic acid mode ==
−
</source>
+
 
 +
=== Settings ===
 +
 
 +
<pre>set cartoon_nucleic_acid_mode, value</pre>
 
{|
 
{|
−
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode0.png|cartoon_nucleic_acid_mode,0|thumb]]
+
!value !! align="left" | effect
−
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode1.png|cartoon_nucleic_acid_mode,1|thumb]]
+
|-
 +
|align="center" |0 || smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain
 +
|-
 +
|align="center" | 1 || smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain
 +
|-
 +
|align="center" | 2 || smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on 5' end and O3' on 3' end (note takes O3' colour at terminus in default colouring)
 +
|-
 +
|align="center" | 3 || appears same as mode 0?
 +
|-
 +
|align="center" | 4 || appears same as mode 2? Seems to be what Pymol uses when it first opens nucleic acid containing file because any other settings change ends and colors. <!--to see this in action open 1e7k and focus on chain c-->
 
|}
 
|}
−
all with:&nbsp;<i>cartoon_ladder_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i>
+
 
−
== cartoon ring finder ==
+
=== Examples ===
−
<source lang="python">
+
 
−
set cartoon_ring_finder, 0 # no ribose, base (or ladder)
 
−
set cartoon_ring_finder, 1 # ribose and base ring
 
−
set cartoon_ring_finder, 2 # base ring only
 
−
</source>
 
 
{|
 
{|
−
|[[Image:DNAcartoon_ringfinder0_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ring_finder,0|thumb]]
+
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_nucleic_acid_mode,0|thumb]]
−
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ring_finder,1|thumb]]
+
|[[Image:DNA-ring3-ladder1-na1-finder1.png|cartoon_nucleic_acid_mode,1|thumb]]
−
|[[Image:DNAcartoon_ringfinder2_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ring_finder,2|thumb]]
+
|[[Image:DNA-ring3-ladder1-na2-finder1.png|cartoon_nucleic_acid_mode,2|thumb]]
 +
|[[Image:DNA-ring3-ladder1-na3-finder1.png|cartoon_nucleic_acid_mode,3|thumb]]
 +
|[[Image:DNA-ring3-ladder1-na4-finder1.png|cartoon_nucleic_acid_mode,4|thumb]]
 
|}
 
|}
−
all with:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0</i>
+
all with:&nbsp;<i>cartoon_ladder_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i>
  
 
[[Category:Nucleic_Acids|Cartoon ring and cartoon ladder settings]]
 
[[Category:Nucleic_Acids|Cartoon ring and cartoon ladder settings]]
 +
[[Category:Representations]]

Latest revision as of 18:31, 27 January 2010

Default settings

The defaults give a phosphate backbone with single sticks passing across the full width of the base plane. 

set cartoon_nucleic_acid_mode, 0 # backbone follows phosphates; actually Pymol itself uses setting '4' as default
set cartoon_ladder_mode, 1 # sticks from backbone into nucleotide
set cartoon_ring_mode, 0 # no nucleotide rings
set cartoon_ring_finder, 1 # ribose and base rings (not displayed since ring mode 0)
default view

Cartoon ring mode

Settings

set cartoon_ring_mode, value
value effect
0 stick from backbone atom to N1 of purines and N3 of pyrimidines
1 simple plane for ribose and base rings covering area between ring bonds
2 simple plane for ribose and base rings covering area inside sticks (slightly smaller than mode 1)
3 plane bounded by sticks for ribose and base rings
4 large sphere of ring diameter at centre of ribose and each base ring
5 small sphere of 1/10 diameter at centre of ribose and each base ring

Examples

cartoon_ring_mode,0
cartoon_ring_mode,1
cartoon_ring_mode,2
cartoon_ring_mode,3
cartoon_ring_mode,4
cartoon_ring_mode,5
all with defaults: cartoon_ladder_mode,1   cartoon_nucleic_acid_mode,0   cartoon_ring_finder,1

Cartoon ring finder

Settings

set cartoon_ring_finder, value
value effect
0 no rings or sticks joining them
1 both ribose and base ring
2 only base ring(s), stick connects directly from phosphate to ring
3 very similar to ring finder 1, slight effect on transparency = distinct behaviour?
4 very similar to ring finder 1: finds ribose and base of nucleotides, and aromatic side chains of proteins
5 sticks visible but rings invisible

Examples

cartoon_ring_finder,0
cartoon_ring_finder,1
cartoon_ring_finder,2
cartoon_ring_finder,3
cartoon_ring_finder,4
cartoon_ring_finder,5

all with: cartoon_ladder_mode,1   cartoon_ring_mode,3   cartoon_nucleic_acid_mode,0

Cartoon ladder mode

Settings

set cartoon_ladder_mode, value
value effect
0 no sticks shown
1 sticks show

Examples

cartoon_ladder_mode,0
cartoon_ladder_mode,1

all with: cartoon_ring_mode,3   cartoon_nucleic_acid_mode,0   cartoon_ring_finder,1

Note that the visibility of the ladder sticks depends on ring mode >0, ring finder >0, nucleic acid mode = 0

Cartoon nucleic acid mode

Settings

set cartoon_nucleic_acid_mode, value
value effect
0 smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain
1 smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain
2 smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on 5' end and O3' on 3' end (note takes O3' colour at terminus in default colouring)
3 appears same as mode 0?
4 appears same as mode 2? Seems to be what Pymol uses when it first opens nucleic acid containing file because any other settings change ends and colors.

Examples

cartoon_nucleic_acid_mode,0
cartoon_nucleic_acid_mode,1
cartoon_nucleic_acid_mode,2
cartoon_nucleic_acid_mode,3
cartoon_nucleic_acid_mode,4

all with: cartoon_ladder_mode,0   cartoon_ring_mode,3   cartoon_ring_finder,1

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