Frequently Asked Questions

[Sakul Ratanalert]

1. I am using the online DAEDALUS portal. Should I still read the documentation for the downloadable MATLAB code?

Yes! The online DAEDALUS portal presents a simplified set of options for users, then sends these inputs to our cluster, which runs DAEDALUS on MATLAB. Most errors that you might reach with the downloadable MATLAB version will still apply for the online portal.

2. I am using a custom PLY file (obtained from an external source such as Blender) and I'm getting an error, such as "Attempted to access start_route(1); index out of bounds because numel(start_route)=0." What should I do?

From the documentation (Step 2.1)

Note: Make sure that the PLY file is a text file and not a binary file. (If you open the PLY file externally, it should be human-readable.) Some PLY files obtained from external sources have been found to have errors, like missing vertices or vertices with coordinates that do not belong to any face. You may use programs such as MeshLab (http://meshlab.sourceforge.net/) to make sure your custom PLY file is correct, or to convert another 3D structure file format into PLY.

3. I created a PLY file from scratch, calculating all of the vertex coordinates, edges, and faces myself. I'm getting an error. What should I do?

[Awesome that you made a PLY file yourself! Don't be discouraged!] The most common error with writing your own PLY file is that the object is not a closed surface, which is what DAEDALUS expects all inputs to be (spherical topologies, toruses, etc). At every point on the surface, you should be able to define an outward normal. A Möbius strip, for example, would not be a valid input. (A Möbius strip with nonzero thickness, however, could be.)

(last updated 2016-Oct-28 by Sakul Ratanalert)

[Eric Henderson]

Hello - I am better at molecules than engineering or math - I am trying to use this tool to generate some simple shapes but so far I have only generated error messages - can you please guide me a bit with respect to the meaning of this message, "Index exceeds matrix dimensions" - thanks! Eric

[Sakul Ratanalert]

Hello! I'm sorry that our error messages are currently not very informative; this is something we are working to improve.

In the meantime, would you be able to attach one of the PLY files you are trying to convert to a following post? I will be able to troubleshoot the problem better this way. Information such as how this PLY file was generated (manually created, obtained from the Internet, etc.) will also be helpful.

Thanks for your patience! 

Sakul