coordinates of dimers based on PDB & PDB1
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3.7 years ago

hi,

I have a challenge of combining a PBD coordinate files with the biological assembly file from the RCBS protein database.

I am able to retrieve the monomer coordinates from the RCBS in PDB format, and have downloaded the associating bioassembly file PDB1. The R package Quartpack allows me to combine the coordinate file with the bio assembly file but doesn't return any intuitive output from the "alignedsuperstructure".

would anyone know of a good way of retrieving the 3d coordinates of eg. a pentamer by combining the coordinate data with the assembly data, and possibly also by selecting the desired assembly, eg bioassembly 3, representing the pentamer. Not necessarily limited to a R solution, but if there exists eg. a known package in R for solving it, it would be great.

Thanks,

Andres

Assembly sequence R • 732 views
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