File Formats
1. caDNAno (.json) file
JSON is the input design file format used for CanDo analysis exported from caDNAno (http://caDNAno.org), which is an open source program that offers rapid prototyping of DNA origami connectivity maps.
2. caDNAno sequence (.csv) file
CSV is the input sequence file format exported from caDNAno.
3. BILD format
BILD is a text file that lists commands for lines, polygons, and geometric primitives used to generate a VRML model in UCSF Chimera. CanDo provides results to users for download including the 3D solution shape, thermal fluctuations of the solution shape, and lowest normal mode shapes using this format where DNA double helices are represented by cylinders. VRML models can be exported from UCSF Chimera for further uses in other visualization programs. More information about the format is available at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html.
4. PDB format
PDB is a text file that lists for each atom its serial number, name, residue sequence number, residue name, chain identifier, and Cartesian coordinates (in Ångströms). CanDo provides a PDB file to users for download if an atomic model of the uploaded caDNAno design is included with the results. A PDB file can be the input of further full atomistic simulations such as molecular dynamics (MD) simulation. More information about the format is available at http://www.wwpdb.org/docs.html.
Tutorial
1. Preparing an input design file using caDNAno
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2. Preparing an input sequence file using caDNAno
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3. Preparing an input sequence file using caDNAno
a. Click the red box (Submit a caDNAno file for analysis…) to expand the submission form
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Modeling Guide
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3D Printing Guide
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