Hi guys
I am toward the end of preparing a pdbx/mmCIF file for an icosahedral viral capsid asymmetric unit. I have noticed most icosahedral capsid mmCIF files are deposited on the PDB as assymetric unit models with biological assemblies embedded into the file, accessible through chimeraX commands such as:
sym #1 assembly 1
I have established the correct symmetry operator to generate my assembly, however I am unsure of how i can embed this assembly into the mmCIF file as "assembly 1" so that it can be accessed through the command listed above?
Thanks,
James.
Check out https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies for a description of the relevant records, in particular the "REMARK 350 BIOMT..." lines that provide the transformation matrices to be applied to the asymmetric unit to generate the capsid.
VIPERdb http://viperdb.scripps.edu may provide some useful tools.
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