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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 will not be visualizedare absent from the visualized atomic model:

We recommend visualizing multi-model PDB files using UCSF Chimera, which properly loads all models: