https://wiki.pymol.org/index.php?title=Examples_of_nucleic_acid_cartoons&feed=atom&action=historyExamples of nucleic acid cartoons - Revision history2024-03-29T11:17:28ZRevision history for this page on the wikiMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=Examples_of_nucleic_acid_cartoons&diff=7947&oldid=prevPyadmin: 1 revision2014-03-28T02:16:23Z<p>1 revision</p>
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</td></tr></table>Pyadminhttps://wiki.pymol.org/index.php?title=Examples_of_nucleic_acid_cartoons&diff=7946&oldid=prevTimmmaaay: /* Settings */2010-01-27T22:31:00Z<p><span dir="auto"><span class="autocomment">Settings</span></span></p>
<p><b>New page</b></p><div>== Default settings ==<br />
The defaults give a phosphate backbone with single sticks passing across the full width of the base plane.<br />
<source lang="python"><br />
set cartoon_nucleic_acid_mode, 0 # backbone follows phosphates; actually Pymol itself uses setting '4' as default<br />
set cartoon_ladder_mode, 1 # sticks from backbone into nucleotide<br />
set cartoon_ring_mode, 0 # no nucleotide rings<br />
set cartoon_ring_finder, 1 # ribose and base rings (not displayed since ring mode 0)<br />
</source><br />
{|<br />
|[[Image:DNA-default-ring0-ladder1-na0-finder1.png|default view|thumb]]<br />
|}<br />
<!-- 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. --><br />
<br />
== Cartoon ring mode ==<br />
<br />
=== Settings ===<br />
<br />
<pre>set cartoon_ring_mode, value</pre><br />
{|}<br />
!value !!align="left"| effect<br />
|-<br />
|align="center" | 0 || stick from backbone atom to N1 of purines and N3 of pyrimidines<br />
|-<br />
|align="center" | 1 || simple plane for ribose and base rings covering area between ring bonds<br />
|-<br />
|align="center" | 2 || simple plane for ribose and base rings covering area inside sticks (slightly smaller than mode 1)<br />
|-<br />
|align="center" | 3 || plane bounded by sticks for ribose and base rings<br />
|-<br />
|align="center" | 4 || large sphere of ring diameter at centre of ribose and each base ring<br />
|-<br />
|align="center" | 5 || small sphere of 1/10 diameter at centre of ribose and each base ring<br />
|}<br />
<br />
=== Examples ===<br />
<br />
{|<br />
|[[Image:DNA-ring0-ladder1-na0-finder1.png|cartoon_ring_mode,0|thumb]]<br />
|[[Image:DNA-ring1-ladder1-na0-finder1.png|cartoon_ring_mode,1|thumb]]<br />
|[[Image:DNA-ring2-ladder1-na0-finder1.png|cartoon_ring_mode,2|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ring_mode,3|thumb]]<br />
|[[Image:DNA-ring4-ladder1-na0-finder1.png|cartoon_ring_mode,4|thumb]]<br />
|[[Image:DNA-ring5-ladder1-na0-finder1.png|cartoon_ring_mode,5|thumb]]<br />
|}<br />
<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><br />
<br />
== Cartoon ring finder ==<br />
<br />
=== Settings ===<br />
<pre>set cartoon_ring_finder, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" | 0 || no rings or sticks joining them<br />
|-<br />
|align="center" | 1 || both ribose and base ring<br />
|-<br />
|align="center" | 2 || only base ring(s), stick connects directly from phosphate to ring<br />
|-<br />
|align="center" | 3 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?<br />
|-<br />
|align="center" | 4 || very similar to ring finder 1: finds ribose and base of nucleotides, and aromatic side chains of proteins<br />
|-<br />
|align="center" | 5 || sticks visible but rings invisible<br />
|}<br />
<br />
=== Examples ===<br />
<br />
{|<br />
|[[Image:DNA-ring3-ladder1-na0-finder0.png|cartoon_ring_finder,0|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ring_finder,1|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder2.png|cartoon_ring_finder,2|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder3.png|cartoon_ring_finder,3|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder4.png|cartoon_ring_finder,4|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder5.png|cartoon_ring_finder,5|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0</i><br />
<br />
== Cartoon ladder mode ==<br />
<br />
=== Settings ===<br />
<br />
<pre>set cartoon_ladder_mode, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" | 0 || no sticks shown<br />
|-<br />
|align="center" | 1 || sticks show<br />
|}<br />
<br />
=== Examples ===<br />
<br />
{|<br />
|[[Image:DNA-ring3-ladder0-na0-finder1.png|cartoon_ladder_mode,0|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ladder_mode,1|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i><br />
<br />
Note that the visibility of the ladder sticks depends on ring mode >0, ring finder >0, nucleic acid mode = 0<br />
<br />
== Cartoon nucleic acid mode ==<br />
<br />
=== Settings ===<br />
<br />
<pre>set cartoon_nucleic_acid_mode, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" |0 || smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain <br />
|-<br />
|align="center" | 1 || smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain<br />
|-<br />
|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)<br />
|-<br />
|align="center" | 3 || appears same as mode 0?<br />
|-<br />
|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--><br />
|}<br />
<br />
=== Examples ===<br />
<br />
{|<br />
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_nucleic_acid_mode,0|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na1-finder1.png|cartoon_nucleic_acid_mode,1|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na2-finder1.png|cartoon_nucleic_acid_mode,2|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na3-finder1.png|cartoon_nucleic_acid_mode,3|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na4-finder1.png|cartoon_nucleic_acid_mode,4|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ladder_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i><br />
<br />
[[Category:Nucleic_Acids|Cartoon ring and cartoon ladder settings]]<br />
[[Category:Representations]]</div>Timmmaaay