Cadnano - Revision history

Doye at 10:56, 24 October 2018

2018-10-24T10:56:35Z

← Older revision		Revision as of 10:56, 24 October 2018
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	Forced crossovers, that is crossovers made by the pencil tool instead of using the default cadnano default positions, will probably create a structure that cannot be relaxed using the input_relax method detailed in the previous section. There is now a way to relax these structures too, by using an alternative interaction_type with a custom interaction term between neighbours on a strand. An example and more detailed description are provided in the ${oxDNA}/EXAMPLES/RELAX_INITIAL_CONFIGURATION/ directory.		Forced crossovers, that is crossovers made by the pencil tool instead of using the default cadnano default positions, will probably create a structure that cannot be relaxed using the input_relax method detailed in the previous section. There is now a way to relax these structures too, by using an alternative interaction_type with a custom interaction term between neighbours on a strand. An example and more detailed description are provided in the ${oxDNA}/EXAMPLES/RELAX_INITIAL_CONFIGURATION/ directory.

	Note that relaxing structures can sometimes be tricky and the difficulty varies depending on the design. It may be necessary to use some trial and error experimentation. As well as changing parameters, options include modifying the cadnano file, and using external forces to guide the origami towards the correct structure.

	== Updated relaxation procedure ==		== Updated relaxation procedure ==
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	:For very large cadnano designs, or for designs of small origamis but with very long unused sections of virtual double helices, the script requires a very large amount of memory which may cause problems.		:For very large cadnano designs, or for designs of small origamis but with very long unused sections of virtual double helices, the script requires a very large amount of memory which may cause problems.

	:~~A large number of insertions or deletions~~ on ~~a small section of dna (where a section is defined~~ as the ~~bases between nodes~~, ~~a node being a crossover or~~ the ~~end of a strand) may create a~~ structure ~~that cannot be relaxed~~.		:Note that relaxing structures can sometimes be tricky and the difficulty varies depending on the design. It may be necessary to use some trial and error experimentation. As well as changing parameters, options include modifying the cadnano file, and using external forces to guide the origami towards the correct structure.

	:~~Very large structures with very frequent crossovers may create a~~ structure ~~that cannot~~ be ~~relaxed~~.		:If the converted structure has topological entanglements of the strands, these are unlikely to be resolved by the relaxation process, because the oxDNA excluded volume interactions prevents strands passing through each other.

Doye: /* Designs with forced crossovers */

2018-10-24T10:51:57Z

Designs with forced crossovers

← Older revision		Revision as of 10:51, 24 October 2018
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	Forced crossovers, that is crossovers made by the pencil tool instead of using the default cadnano default positions, will probably create a structure that cannot be relaxed using the input_relax method detailed in the previous section. There is now a way to relax these structures too, by using an alternative interaction_type with a custom interaction term between neighbours on a strand. An example and more detailed description are provided in the ${oxDNA}/EXAMPLES/RELAX_INITIAL_CONFIGURATION/ directory.		Forced crossovers, that is crossovers made by the pencil tool instead of using the default cadnano default positions, will probably create a structure that cannot be relaxed using the input_relax method detailed in the previous section. There is now a way to relax these structures too, by using an alternative interaction_type with a custom interaction term between neighbours on a strand. An example and more detailed description are provided in the ${oxDNA}/EXAMPLES/RELAX_INITIAL_CONFIGURATION/ directory.

	Note that ~~using this interaction to relax~~ structures can be tricky and the difficulty varies depending on the design. It may be necessary to use ~~a lot of~~ trial and error, ~~to modify~~ the cadnano file, and ~~to use~~ external forces to guide the origami towards the correct structure.		Note that relaxing structures can sometimes be tricky and the difficulty varies depending on the design. It may be necessary to use some trial and error experimentation. As well as changing parameters, options include modifying the cadnano file, and using external forces to guide the origami towards the correct structure.

	== Updated relaxation procedure ==		== Updated relaxation procedure ==

Doye: /* Updated relaxation procedure */

2018-10-24T10:13:04Z

Updated relaxation procedure

← Older revision		Revision as of 10:13, 24 October 2018
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	== Updated relaxation procedure ==		== Updated relaxation procedure ==

	The latest recommended approach to relaxing origamis and other structures can be found ~~here:~~ ${oxDNA}/EXAMPLES/~~RELAX_INITIAL_CONFIGURATION~~/ directory.		The latest recommended approach to relaxing origamis and other structures can be found in the ${oxDNA}/EXAMPLES/NEW_RELAX_PROCEDURE/ directory.

	== Choosing the sequence ==		== Choosing the sequence ==

Doye at 10:10, 24 October 2018

2018-10-24T10:10:50Z

← Older revision		Revision as of 10:10, 24 October 2018
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	Note that using this interaction to relax structures can be tricky and the difficulty varies depending on the design. It may be necessary to use a lot of trial and error, to modify the cadnano file, and to use external forces to guide the origami towards the correct structure.		Note that using this interaction to relax structures can be tricky and the difficulty varies depending on the design. It may be necessary to use a lot of trial and error, to modify the cadnano file, and to use external forces to guide the origami towards the correct structure.


	== Updated relaxation procedure ==		== Updated relaxation procedure ==

Doye at 10:10, 24 October 2018

2018-10-24T10:10:17Z

← Older revision		Revision as of 10:10, 24 October 2018
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	Note that using this interaction to relax structures can be tricky and the difficulty varies depending on the design. It may be necessary to use a lot of trial and error, to modify the cadnano file, and to use external forces to guide the origami towards the correct structure.		Note that using this interaction to relax structures can be tricky and the difficulty varies depending on the design. It may be necessary to use a lot of trial and error, to modify the cadnano file, and to use external forces to guide the origami towards the correct structure.


			== Updated relaxation procedure ==

			The latest recommended approach to relaxing origamis and other structures can be found here: ${oxDNA}/EXAMPLES/RELAX_INITIAL_CONFIGURATION/ directory.

	== Choosing the sequence ==		== Choosing the sequence ==

Engel: /* Choosing the sequence */

2016-05-26T17:29:09Z

Choosing the sequence

← Older revision		Revision as of 17:29, 26 May 2016
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	== Choosing the sequence ==		== Choosing the sequence ==

	By default, a scaffold strand with a random sequence is generated. It is possible to set the sequence instead. The script looks for a file containing the sequence called "caca.sqs". That file should contain a letter (A,T,G,C or R for random) designating the sequence of the scaffold strand, for every pair of squares (which denote a base pair) in the cadnano design. This includes squares that do not contain a strand. So the sequence file should be an M by N grid of letters where M is the length of the helices and N is the number of helices in the cadnano design.		By default, a scaffold strand with a random sequence is generated. It is possible to set the sequence instead. The script looks for a file containing the sequence called "caca.sqs". That file should contain a letter (A,T,G,C or R for random) designating the sequence of the scaffold strand, for every pair of squares (which denote a base pair) in the cadnano design. This includes squares that do not contain a strand. So the sequence file should be an M by N grid of letters where M is the length of the helices and N is the number of helices in the cadnano design (including entirely unoccupied rows). Note that there is no need to include skips in the sequence file.

	== Limitations ==		== Limitations ==

Snodinb: /* Choosing the sequence */

2015-08-23T09:27:35Z

Choosing the sequence

← Older revision		Revision as of 09:27, 23 August 2015
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	== Choosing the sequence ==		== Choosing the sequence ==

	By default, a ~~structure~~ with a random sequence is generated. It is possible to set the sequence instead. The script looks for a file containing the sequence called "caca.sqs". That file should contain a letter (A,T,G,C or R for random) designating the sequence of the scaffold strand, for every pair of squares (which denote a base pair) in the cadnano design. This includes squares that do not contain a strand. So the sequence file should be an M by N grid of letters where M is the length of the helices and N is the number of helices in the cadnano design.		By default, a scaffold strand with a random sequence is generated. It is possible to set the sequence instead. The script looks for a file containing the sequence called "caca.sqs". That file should contain a letter (A,T,G,C or R for random) designating the sequence of the scaffold strand, for every pair of squares (which denote a base pair) in the cadnano design. This includes squares that do not contain a strand. So the sequence file should be an M by N grid of letters where M is the length of the helices and N is the number of helices in the cadnano design.

	== Limitations ==		== Limitations ==

Snodinb at 09:25, 23 August 2015

2015-08-23T09:25:49Z

← Older revision		Revision as of 09:25, 23 August 2015
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	For the tile discussed above, the configuration files before and after relaxation, as well as the topology file, can be found in ${oxDNA}/EXAMPLES/CADNANO_INTERFACE/TILE/.		For the tile discussed above, the configuration files before and after relaxation, as well as the topology file, can be found in ${oxDNA}/EXAMPLES/CADNANO_INTERFACE/TILE/.

			== Designs with forced crossovers ==

			Forced crossovers, that is crossovers made by the pencil tool instead of using the default cadnano default positions, will probably create a structure that cannot be relaxed using the input_relax method detailed in the previous section. There is now a way to relax these structures too, by using an alternative interaction_type with a custom interaction term between neighbours on a strand. An example and more detailed description are provided in the ${oxDNA}/EXAMPLES/RELAX_INITIAL_CONFIGURATION/ directory.

			Note that using this interaction to relax structures can be tricky and the difficulty varies depending on the design. It may be necessary to use a lot of trial and error, to modify the cadnano file, and to use external forces to guide the origami towards the correct structure.

			== Choosing the sequence ==

			By default, a structure with a random sequence is generated. It is possible to set the sequence instead. The script looks for a file containing the sequence called "caca.sqs". That file should contain a letter (A,T,G,C or R for random) designating the sequence of the scaffold strand, for every pair of squares (which denote a base pair) in the cadnano design. This includes squares that do not contain a strand. So the sequence file should be an M by N grid of letters where M is the length of the helices and N is the number of helices in the cadnano design.

	== Limitations ==		== Limitations ==

	~~The majority of structures without forced crossovers should work. However there are limitations:~~

	:For very large cadnano designs, or for designs of small origamis but with very long unused sections of virtual double helices, the script requires a very large amount of memory which may cause problems.		:For very large cadnano designs, or for designs of small origamis but with very long unused sections of virtual double helices, the script requires a very large amount of memory which may cause problems.

	:A large number of insertions or deletions on a small section of dna (where a section is defined as the bases between nodes, a node being a crossover or the end of a strand) may create a structure that cannot be relaxed.		:A large number of insertions or deletions on a small section of dna (where a section is defined as the bases between nodes, a node being a crossover or the end of a strand) may create a structure that cannot be relaxed.

	~~:Forced crossovers, that is crossovers made by the pencil tool instead of using the default cadnano default positions, will probably create a structure that cannot be relaxed.~~

	:Very large structures with very frequent crossovers may create a structure that cannot be relaxed.		:Very large structures with very frequent crossovers may create a structure that cannot be relaxed.

Romano at 11:37, 16 May 2012

2012-05-16T11:37:43Z

← Older revision		Revision as of 11:37, 16 May 2012
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	[[Category:Examples]]		[[Category:Examples]]
	[http://cadnano.org ~~cadnano~~] is a tool for designing DNA origami structures. oxDNA includes an interface that allows origami designs generated in cadnano to be used as starting configurations for simulation. ~~cadnano~~ can also be used in this way to make non-origami structures such as DNA tiles for use in the model.		[http://cadnano.org Cadnano] is a tool for designing DNA origami structures. oxDNA includes an interface that allows origami designs generated in cadnano to be used as starting configurations for simulation. Cadnano can also be used in this way to make non-origami structures such as DNA tiles for use in the model.

	== Example: DX tile ==		== Example: DX tile ==
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	The tile design is now finished and ready to be used as a starting configuration for simulation after some processing. The design can be found at ${oxDNA}/EXAMPLES/CADNANO_INTERFACE/TILE/tile.json.		The tile design is now finished and ready to be used as a starting configuration for simulation after some processing. The design can be found at ${oxDNA}/EXAMPLES/CADNANO_INTERFACE/TILE/tile.json.

	== Using ~~cadnano~~ Designs as Starting Configurations for oxDNA ==		== Using Cadnano Designs as Starting Configurations for oxDNA ==

	The script candnano_interface.py is used to generate an oxDNA configuration and topology file from a cadnano design. In addition it creates some files containing information about the origami that can be useful later for analysing its trajectory. Its usage is		The script candnano_interface.py is used to generate an oxDNA configuration and topology file from a cadnano design. In addition it creates some files containing information about the origami that can be useful later for analysing its trajectory. Its usage is

Romano at 11:36, 16 May 2012

2012-05-16T11:36:12Z

← Older revision		Revision as of 11:36, 16 May 2012
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	[[Category:Examples]]		[[Category:Examples]]
	[http://cadnano.org ~~Cadnano~~] is a tool for designing DNA origami structures. oxDNA includes an interface that allows origami designs generated in ~~Cadnano~~ to be used as starting configurations for simulation. ~~Cadnano~~ can also be used in this way to make non-origami structures such as DNA tiles for use in the model.		[http://cadnano.org cadnano] is a tool for designing DNA origami structures. oxDNA includes an interface that allows origami designs generated in cadnano to be used as starting configurations for simulation. cadnano can also be used in this way to make non-origami structures such as DNA tiles for use in the model.

	== Example: DX tile ==		== Example: DX tile ==
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	http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/tilechimera.png		http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/tilechimera.png

	The use of ~~Cadnano~~ for the purpose of creating starting configurations will be illustrated using a tile similar to the DX tile. In this case ~~Cadnano~~ 2 will be used to design the tile, although the original ~~Cadnano~~ operates in a similar way and is fully compatible with the interface to oxDNA. Note that, while using cadnano, any unwanted actions can be undone with ctrl+z (this feature is new in ~~Cadnano~~ 2).		The use of cadnano for the purpose of creating starting configurations will be illustrated using a tile similar to the DX tile. In this case cadnano 2 will be used to design the tile, although the original cadnano operates in a similar way and is fully compatible with the interface to oxDNA. Note that, while using cadnano, any unwanted actions can be undone with ctrl+z (this feature is new in cadnano 2).

	First click the blue "add new square lattice" button on the toolbar - a new square lattice will be created in the lattice view. The circles represent a cross-sectional view of potential DNA double helices on the square lattice. Create two empty virtual double helices in the path view by clicking on any two adjacent circles, one on top of the other. Next, using the pencil tool from the toolbar on the right, fill in all four rows in the path view by dragging from one end of each row to the other. Each double helix has two rows, and each row represents one of the strands of a double helix.		First click the blue "add new square lattice" button on the toolbar - a new square lattice will be created in the lattice view. The circles represent a cross-sectional view of potential DNA double helices on the square lattice. Create two empty virtual double helices in the path view by clicking on any two adjacent circles, one on top of the other. Next, using the pencil tool from the toolbar on the right, fill in all four rows in the path view by dragging from one end of each row to the other. Each double helix has two rows, and each row represents one of the strands of a double helix.
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	The tile design is now finished and ready to be used as a starting configuration for simulation after some processing. The design can be found at ${oxDNA}/EXAMPLES/CADNANO_INTERFACE/TILE/tile.json.		The tile design is now finished and ready to be used as a starting configuration for simulation after some processing. The design can be found at ${oxDNA}/EXAMPLES/CADNANO_INTERFACE/TILE/tile.json.

	== Using ~~Cadnano~~ Designs as Starting Configurations for oxDNA ==		== Using cadnano Designs as Starting Configurations for oxDNA ==

	The script candnano_interface.py is used to generate an oxDNA configuration and topology file from a cadnano design. In addition it creates some files containing information about the origami that can be useful later for analysing its trajectory. Its usage is		The script candnano_interface.py is used to generate an oxDNA configuration and topology file from a cadnano design. In addition it creates some files containing information about the origami that can be useful later for analysing its trajectory. Its usage is
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	The majority of structures without forced crossovers should work. However there are limitations:		The majority of structures without forced crossovers should work. However there are limitations:

	:For very large ~~Cadnano~~ designs, or for designs of small origamis but with very long unused sections of virtual double helices, the script requires a very large amount of memory which may cause problems.		:For very large cadnano designs, or for designs of small origamis but with very long unused sections of virtual double helices, the script requires a very large amount of memory which may cause problems.

	:A large number of insertions or deletions on a small section of dna (where a section is defined as the bases between nodes, a node being a crossover or the end of a strand) may create a structure that cannot be relaxed.		:A large number of insertions or deletions on a small section of dna (where a section is defined as the bases between nodes, a node being a crossover or the end of a strand) may create a structure that cannot be relaxed.