Biomod/2011/Harvard/HarvarDNAnos:caDNAnoFiles

Scaffold Permutation Analysis
For reverse engineering of origami without caDNAno specifications into JSON format
 * This Python script can be used to determine if reverse-engineered staples match those provided by the relevant literature reference:
 * [[Media:Sphere debug.zip]]
 * Guidelines:
 * You'll need to match the file name convention and directory structure in the .zip file

SphereCADv.2
For determining orientation and visualizing the location of staple strands contained within the sphere outlined by Han, et. al. in 
 * Download SphereCADv.2, and adress all questions/comments to Nicholas Perkons at nperkons@college.harvard.edu. The .zip file contains all necessary files to run the caDNAno file and a .txt file containing instructions on how to run the program, which is also outlined below:
 * 1.	Download SphereCADv2.zip from .


 * 2.	Download these additional programs to read the files contained within:
 * Microsoft Office (or OpenOffice ),
 * caDNAno [square lattice] ,
 * AutoCAD  (NOTE: free to students with a ".edu" e-mail at ),
 * Adobe PDF Reader .


 * 3.	Open SphereCADv.2_Excel.xlsx and choose your input option:
 * Option 1: caDNAno coordinates
 * Option 2: Han's supplementary info coordinates (Note: The innermost ring refers to helices 1 and 24 as the second-innermost ring refers to helices 2 and 23)
 * Option 3: AutoCAD coordinates (X,Y,Z)


 * Option 1: caDNAno
 * 4_1.	Open SphereCadv.2_caDNAno.json using caDNAno [square lattice]
 * 5_1.	Determine the helix and base number within the file of the base in question
 * 6_1.	Plug above retrieved information into SphereCADv.2_Excel.xlsx


 * Option 2: SuppInfo
 * 4_2.	Open SphereCadv.2_HanSuppInfo.pdf or visit page S114 
 * 5_2.	Determine the helix and base number within the document of the base in question (Note: The innermost ring refers to helices 1 and 24 as the second-innermost ring refers to helices 2 and 23)
 * 6_2.	Plug above retrieved information into SphereCADv.2_Excel.xlsx


 * Option 3: AutoCAD
 * 4_3.	Open SphereCadv.2_AutoCAD.dwg
 * 5_3.	Determine the X,Y and Z coordinates of the base in question by clicking on the base in question in the above document (a blue square will appear to cover the base upon doing so), then right click on the object, select properties, and record the base's X,Y,Z coordinates
 * NOTE: Before continuing to select another object, press CMD+Z to get rid of the blue square
 * 6_3.	Plug above retrieved information into SphereCADv.2_Excel.xlsx


 * 7.	Enjoy the calculated outputs that can be found in the blue (or yellow in the case of staple orientation) colored cells


 * 8.	To highlight bases in AutoCAD acquired as an output from Options 1 or 2, type the following commands into the command line within Autocad (press return after each entry):
 * Sphere
 * X,Y,Z (e.g. "1.023,2.034,3.045")
 * .15
 * (Note: To remove highlighting press "CMD+Z")


 * Additional Notes:
 * Information and formulas contained within SphereCADv.2_Excel.xlsx can be traced to data values contained within CoordinatesSpreadsheet_Sphere.xlsx.
 * SphereCadv.2_HanSuppInfo.pdf taken from page S114 of 
 * SuppInfo always refers to the Supplementary Information section of the recent Science paper published by Han, et. al 
 * In all documents contained within SphereCADv.2.zip that reference "SuppInfo," the innermost ring of the figure contained within refers to helices 1 and 24 as the second-innermost ring refers to helices 2 and 23
 * Credits:
 * SphereCADv.2 was organized by the 2011 Harvard BioMod Team , which includes: Nicholas Perkons, Sherrie Wang, Evan Wu, and Shwinn Ricci with additional help from Harvard Biophysics Ph.D candidate and team mentor Adam Marblestone
 * DNA Origami with Complex Curvatures in Three-Dimensional Space. Han, et. al.  Science:  15 April 2011 .
 * SphereCadv.2_caDNAno.json (caDNAno reference file). Sherrie Wang.  Created June 2011.
 * CoordinatesSpreadsheet_Sphere.xlsx. Nicholas Perkons.  Created June 2011.
 * SphereCADv.2_AutoCAD.dwg. Nicholas Perkons.  Created July 2011.
 * SphereCADv.2_Excel.xlsx. Nicholas Perkons.  Created July 2011.

Using SphereCADBasic (SphereCADv.1)

 * 1) Download SphereCADBasic and open with Microsoft Excel or a compatible spreadsheet viewer (e.g. OpenOffice, NOTE: GoogleDocs cannot open this file)
 * 2) Use any of the three available input options:  caDNAno coordinates, Han's Supplementary Info coordinates, or Maya 3D Coordinates
 * [[Media:Sphere match.json | caDNAno Sphere File]]
 * Han's Supplementary Info, see page S114 and the high-resolution version of the same schematic at the end of this PDF
 * Maya File Coming Soon!

caDNAno File Repository
Dear Members of the DNA Origami Community: Please feel free to upload your .JSON files here!

Sphere

 * JSON file: [[Media:Sphere match.json]]
 * Literature reference: [recent Science paper by Han et al.]
 * Scaffold sequence propagation instructions: add [[Media:M13mp18_new.txt‎]] as a custom sequence
 * See this excel file for a way to map between caDNAno coordinates, Han's coordinate system, theta/phi position, and the direction the staple helix is pointing

Tall Rectangular Origami

 * JSON file: [[Media:rothemund-tallrect.json]]
 * Literature reference: http://www.nature.com/nature/journal/v440/n7082/abs/nature04586.html

Rectangular Origami

 * JSON file: [[Media:rothemund-rect.json]]
 * Literature reference: http://www.nature.com/nature/journal/v440/n7082/abs/nature04586.html

Long Rectangular Origami

 * JSON file: [[Media:jungmann-lro.json]]
 * Literature reference: http://pubs.acs.org/doi/abs/10.1021/nl103427w

180-degree curved 6-helix bundle

 * Tutorial on 6hb curvature

Cylinder with Opening in Middle (Wu, June 2011)

 * JSON file: [[Media:Boxwithmiddleopening.json]]

Box with Lid and Locking Mechanism (Wu, June 2011)

 * JSON file: [[Media:Boxwithlid parlockmechanism-edited.json]]
 * [[Media:Boxwithlid parlockmechanism schematic.jpg | Schematic]]

Box with Opening in Middle (Perkons, June 2011)

 * JSON File: [[Media:Perkons_Box1.json]]
 * [[Media:Perkonsfbook2.jpg | Schematic]]

Sphere with Outward Pointing Broken Staple Seams (Perkons, June 2011)

 * [[Media: Sphere_OutwardPointingBrokenSeams.json]]

Five-sided Continuous Box without Lid (Perkons, June 2011)

 * [[Media:Perkons_OpenBox.json]]

 