Overview of nucleic acid cartoons - Revision history

Bell: 4 revisions

2016-02-08T05:26:50Z

4 revisions

Speleo3: Third-party Wrappers

2016-01-22T22:05:46Z

Third-party Wrappers

Pyadmin: 1 revision

2014-03-28T02:16:34Z

1 revision

Wayne461: /* Nucleic acid mode */

2009-04-17T22:45:38Z

Nucleic acid mode

Aflaus: Nucleic acid cartoon settings moved to Overview of nucleic acid cartoons

2007-12-09T18:28:44Z

Nucleic acid cartoon settings moved to Overview of nucleic acid cartoons

Aflaus at 18:22, 9 December 2007

2007-12-09T18:22:59Z

Aflaus: New page: == Overview == Pymol has a complex group of settings for controlling the way nucleic acids are represented, broadly separated into: * ring, for ribose and base ring(s) * ladder, for the s...

2007-12-09T17:48:18Z

New page: == Overview == Pymol has a complex group of settings for controlling the way nucleic acids are represented, broadly separated into: * ring, for ribose and base ring(s) * ladder, for the s...

New page

== Overview ==

Pymol has a complex group of settings for controlling the way nucleic acids are represented, broadly separated into:
* ring, for ribose and base ring(s)
* ladder, for the sticks connecting the backbone, ribose and base ring(s)
* nucleic acid, for the smooth backbone path

Each setting can be altered with the set command, for example:
<pre>set cartoon_ring_mode, 1</pre>

The cartoon settings affect each other so experimentation may be necessary to achieve what you want. many of the mode settings only seem to work at the global level and cannot be applied to individual objects or selections.

== Ring settings ==

=== Ring mode ===

Ring mode defines the representation of the ribose and base.

{|
!cartoon_ring_mode !! 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
|-
|align="center" | 6+ || appears to default to ring mode 2
|}
=== Ring finder ===

Ring finder defines the rings which are recognised

{|
!cartoon_ring_finder !! 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 rin
|-
|align="center" | 3 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?
|-
|align="center" | 4 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?
|-
|align="center" | 5 || sticks visible but rings invisible
|-
|align="center" | 6+ || appears to default to ring finder 5
|}

==== Other settings for rings ====

{|
|cartoon_ring_color || color || set the colour of the ring or sphere
|-
|cartoon_ring_width || float || thickness of ring for planes and sticks (modes 1, 2, 3)
|-
|cartoon_ring_radius || float || radius of ring for spheres (modes 4, 5), negative number gives sphere of same radius as ring for mode 4, approx 1/10 ring diameter mode 5
|-
|cartoon_ring_transparency || float || transparency of ring or sphere, does not affect sticks in ring mode 3
|}

=== Ladder settings ===

==== Ladder mode ====

Ladder mode affects the sticks connecting the backbone to ribose and ribose to base, and ring mode 0 or ring finder 5.

cartoon_ladder_mode 0 no sticks shown
cartoon_ladder_mode 1 sticks shown
cartoon_ladder_mode 2+ appears to default to ladder mode 1

==== Other settings for ladder ====

cartoon_ladder_color color colour of the stick
cartoon_ladder_radius float stick width for ring modes 1, 4 and 5 (default is 0.25), in other ring modes the ladder stick width is controlled by the ring width instead

=== Nucleic acid settings ===

==== Nucleic acid mode ====

cartoon_nucleic_acid_mode 0 smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain
cartoon_nucleic_acid_mode 1 smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain
cartoon_nucleic_acid_mode 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)
cartoon_nucleic_acid_mode 3 appears same as mode 0?
cartoon_nucleic_acid_mode 4 appears same as mode 2?
cartoon_nucleic_acid_mode 5+ appears to defult to nucleic acid mode 0
ribbon_nucleic_acid_mode has the equivalent behaviour to cartoon_nucleic_acid_mode

==== Other settings for nucleic acid ====

cartoon_nucleic_acid_color color backbone colour (default is backbone atom colour)

← Older revision		Revision as of 22:05, 22 January 2016
Line 127:		Line 127:
	\|align="center" \| color \|\| color \|\| backbone colour (default is backbone atom colour)		\|align="center" \| color \|\| color \|\| backbone colour (default is backbone atom colour)
	\|}		\|}
		+
		+	== Third-party Wrappers ==
		+
		+	* [[dssr_block]] can create "block" shaped base pair cartoons with DSSR

@@ Line 107: / Line 107: @@
 |align="center" | 3 || appears same as mode 0
 |-
-|align="center" | 4 || appears same as mode 2?
+|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-->
 |-
 |align="center" | 5+ || appears to defult to nucleic acid mode 0

← Older revision	Revision as of 05:26, 8 February 2016
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← Older revision	Revision as of 02:16, 28 March 2014
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← Older revision	Revision as of 18:28, 9 December 2007
(No difference)

@@ Line 6: / Line 6: @@
 * nucleic acid, for the smooth backbone path
-Each setting can be altered with the set command, for example:
+Each setting can be altered with the set command. The cartoon settings affect each other so experimentation may be necessary to achieve what you want. Many of the mode settings only seem to work at the global level and cannot be applied to individual objects or selections.
 == Ring settings ==
@@ Line 16: / Line 13: @@
 Ring mode defines the representation of the ribose and base.
+<pre>set cartoon_ring_mode, value</pre>
 {|
-!cartoon_ring_mode !! align="left" | effect
+!value !!align="left"|  effect
 |-
 |align="center" | 0 || stick from backbone atom to N1 of purines and N3 of pyrimidines
@@ Line 37: / Line 34: @@
 Ring finder defines the rings which are recognised
+<pre>set cartoon_ring_finder, value</pre>
 {|
-!cartoon_ring_finder !! align="left" | effect
+!value !! align="left" | effect
 |-
 |align="center" | 0 || no rings or sticks joining them
@@ Line 45: / Line 42: @@
 |align="center" | 1 || both ribose and base ring
 |-
-|align="center" | 2 || only base ring(s), stick connects directly from phosphate to rin
+|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?
@@ Line 56: / Line 53: @@
 |}
-==== Other settings for rings ====
+=== Other settings for ring ===
+<pre>set cartoon_ring_xxx, value</pre>
 {|
-|cartoon_ring_color || color || set the colour of the ring or sphere
+! align="center" | xxx !! value !! align="left" | effect
 |-
-|cartoon_ring_width || float || thickness of ring for planes and sticks (modes 1, 2, 3)
+|align="center" | color || align="center" |color || set the colour of the ring or sphere
 |-
-|cartoon_ring_radius || float || radius of ring for spheres (modes 4, 5), negative number gives sphere of same radius as ring for mode 4, approx 1/10 ring diameter mode 5
+|align="center" | width || align="center" | float || thickness of ring for planes and sticks (modes 1, 2, 3)
 |-
-|cartoon_ring_transparency || float || transparency of ring or sphere, does not affect sticks in ring mode 3
+|align="center" | radius ||  align="center" |float || radius of ring for spheres (modes 4, 5), negative number gives sphere of same radius as ring in mode 4, approx 1/10 ring diameter in mode 5
 |}
-=== Ladder settings ===
+== Ladder settings ==
-==== Ladder mode ====
+=== Ladder mode ===
 Ladder mode affects the sticks connecting the backbone to ribose and ribose to base, and ring mode 0 or ring finder 5.
-cartoon_ladder_mode	0	no sticks shown
+== Nucleic acid settings ==
-==== Other settings for ladder ====
+=== Nucleic acid mode ===
-cartoon_ladder_color	color	colour of the stick
+=== Other settings for nucleic acid ===
-cartoon_ladder_radius	float	stick width for ring modes 1, 4 and 5 (default is 0.25), in other ring modes the ladder stick width is controlled by the ring width instead
+<pre>set cartoon_nucleic_acid_xxx, value</pre>
+{|
-=== Nucleic acid settings ===
+! xxx !! value !! align="left" | effect
+|-
-==== Nucleic acid mode ====
+|align="center" | color || color || backbone colour (default is backbone atom colour)
+|}