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2014-03-28T02:16:23Z

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Timmmaaay: /* Settings */

2010-01-27T22:31:00Z

Settings

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== Default settings ==
The defaults give a phosphate backbone with single sticks passing across the full width of the base plane.
<source lang="python">
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)
</source>
{|
|[[Image:DNA-default-ring0-ladder1-na0-finder1.png|default view|thumb]]
|}


== Cartoon ring mode ==

=== Settings ===

<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:DNA-ring0-ladder1-na0-finder1.png|cartoon_ring_mode,0|thumb]]
|[[Image:DNA-ring1-ladder1-na0-finder1.png|cartoon_ring_mode,1|thumb]]
|[[Image:DNA-ring2-ladder1-na0-finder1.png|cartoon_ring_mode,2|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: cartoon_ladder_mode,1   cartoon_nucleic_acid_mode,0   cartoon_ring_finder,1</center>

== Cartoon ring finder ==

=== Settings ===
<pre>set cartoon_ring_finder, value</pre>
{|
!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: cartoon_ladder_mode,1   cartoon_ring_mode,3   cartoon_nucleic_acid_mode,0

== 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:DNA-ring3-ladder0-na0-finder1.png|cartoon_ladder_mode,0|thumb]]
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ladder_mode,1|thumb]]
|}
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 ===

<pre>set cartoon_nucleic_acid_mode, value</pre>
{|
!value !! align="left" | effect
|-
|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. 
|}

=== Examples ===

{|
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_nucleic_acid_mode,0|thumb]]
|[[Image:DNA-ring3-ladder1-na1-finder1.png|cartoon_nucleic_acid_mode,1|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: cartoon_ladder_mode,0   cartoon_ring_mode,3   cartoon_ring_finder,1

[[Category:Nucleic_Acids|Cartoon ring and cartoon ladder settings]]
[[Category:Representations]]

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Examples of nucleic acid cartoons - Revision history

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Timmmaaay: /* Settings */