Examples of nucleic acid cartoons: Difference between revisions
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all with defaults: cartoon_ladder_mode,1 cartoon_nucleic_acid_mode,0 cartoon_ring_finder,1
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== | == 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, | 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 | set cartoon_ring_finder, 1 # ribose and base rings (not displayed since ring mode 0) | ||
</source> | </source> | ||
{| | {| | ||
|[[Image: | |[[Image:DNA-default-ring0-ladder1-na0-finder1.png|default view|thumb]] | ||
|} | |} | ||
== | <!-- 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. --> | ||
< | |||
== 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: | |[[Image:DNA-ring0-ladder1-na0-finder1.png|cartoon_ring_mode,0|thumb]] | ||
|[[Image: | |[[Image:DNA-ring1-ladder1-na0-finder1.png|cartoon_ring_mode,1|thumb]] | ||
|[[Image: | |[[Image:DNA-ring2-ladder1-na0-finder1.png|cartoon_ring_mode,2|thumb]] | ||
|[[Image: | |[[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: <i>cartoon_ladder_mode,1 cartoon_nucleic_acid_mode,0 cartoon_ring_finder,1</i></center> | <center>all with defaults: <i>cartoon_ladder_mode,1 cartoon_nucleic_acid_mode,0 cartoon_ring_finder,1</i></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: <i>cartoon_ladder_mode,1 cartoon_ring_mode,3 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: | |[[Image:DNA-ring3-ladder0-na0-finder1.png|cartoon_ladder_mode,0|thumb]] | ||
|[[Image: | |[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ladder_mode,1|thumb]] | ||
|} | |} | ||
all with: <i>cartoon_ring_mode,3 cartoon_nucleic_acid_mode,0 cartoon_ring_finder,1</i> | all with: <i>cartoon_ring_mode,3 cartoon_nucleic_acid_mode,0 cartoon_ring_finder,1</i> | ||
== | |||
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, | == 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. <!--to see this in action open 1e7k and focus on chain c--> | |||
|} | |} | ||
== | === Examples === | ||
{| | {| | ||
|[[Image: | |[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_nucleic_acid_mode,0|thumb]] | ||
|[[Image: | |[[Image:DNA-ring3-ladder1-na1-finder1.png|cartoon_nucleic_acid_mode,1|thumb]] | ||
|[[Image: | |[[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: <i>cartoon_ladder_mode, | all with: <i>cartoon_ladder_mode,0 cartoon_ring_mode,3 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)
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 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
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
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
all with: cartoon_ladder_mode,0 cartoon_ring_mode,3 cartoon_ring_finder,1