Dear CanDo Users,
This Wiki page is created for you to post common questions and answers.
Q1. Why do I only see part of the atomic model CanDo created from my design?
A1. CanDo saves an atomic model it creates as a multi-model PDB file, in which each DNA strand is an individual model. As an example, this atomic model (tutorial_v2_multimodel.pdb) consists of four DNA strands saved as Models 1-4. Some molecular visualization software, such as VMD, only load the first model by default. Thus, Models 2-4 in this example are absent from the visualized atomic model:
We recommend visualizing multi-model PDB files using UCSF Chimera, which properly loads all models:
CanDo Development Team, Laboratory for Computational Biology and Biophysics, MIT