Structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant

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De novo protein design by deep network hallucination (2020, methodology): “Manual rebuilding in Coot 55 and cycles of Phenix refinement 56 were used to build the final model.”
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “In the Phenix GUI, the results from all specific validations are seamlessly integrated with the graphics programs Coot and PyMOL (Fig.”
Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “…sum of related H and D occupancies is 1. phenix.refine does not currently build alternative conformations or H/D sites; external tools can be used for this, such as phenix.ready_set to add H/D atoms or Coot (Emsley & Cowtan, 2004; Emsley et al., 2010) to add side chains in alternate conformations.”
Overview of the CCP4 suite and current developments (2011, methodology): “Rather than simply reviewing the results of previously run programs and performing interactive model editing, Coot (Emsley et al., 2010) can launch separate refinement and validation programs (Fig.”