Biomod/2011/Harvard/HarvarDNAnos:SphereCAD

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SphereCAD

Current Edition

SphereCADv.3.1 (TBA)

3-D sphere to be replaced with 24 concentric DNA rings

SphereCADv.3 (2011-08-16)

Instead of using BASIC and Maya3D, a completely independent graphical user interface (GUI) that integrates the 2-dimensional caDNAno image with a 3-dimensional sphere render, complete with free camera rotation. Coded exclusively in python.

Incorporates wxPython and PyOpenGL packages while utilizing the wx.WindowSplitter module extensively to create the effect of two windows in one.
Once the 2-dimensional caDNAno design is incorporated into the GUI, this build will be complete. Download links forthcoming.

SphereCADv.2 (2011-07-11)

For determining orientation and visualizing the location of staple strands contained within the sphere outlined by Han, et. al. here.

  • Download SphereCADv.2, and address 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 here.
2. Download these additional programs to read the files contained within:
Microsoft Office (or OpenOffice)
caDNAno
AutoCAD (Note: Free to students with a ".edu" e-mail!)
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 <http://biodesign.asu.edu/assets/files/3dorigami-highresolution-si.pdf>
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 <http://biodesign.asu.edu/assets/files/3dorigami-highresolution-si.pdf>
    • SuppInfo always refers to the Supplementary Information section of the recent Science paper published by Han, et. al <http://www.sciencemag.org/content/332/6027/342.full>
    • 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 <http://openwetware.org/wiki/Biomod/2011/Harvard/HarvarDNAnos>, 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 <http://www.sciencemag.org/content/332/6027/342.full>.
    • 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.

Older Editions

SphereCADBasic (2011-07-06)

  • Using SphereCADBasic
  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, Supplementary Info Coordinates, or Maya 3D Coordinates
caDNAno Sphere File
Han's Supplementary Info, see page S142
Maya File Coming Soon!

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