3D Structure Refinement Workflow
Stereochemical & backbone building errors are common in medium-resolution experimental structures of RNAs due to the difficulty and tedium of manually fitting coordinates into density maps. We maintain tools to help correct these errors automatically.
Prepare your map from cryoEM or crystallography and starting coordinates.
Carry out ERRASER either via server, on your laptop with Rosetta, or as part of PHENIX.
[Coming soon: Test that your structure are consistent with one-dimensional chemical accessibility data easily acquired with this basic workflow. E-mail us if interested.]
The publicly available version of ERRASER does not handle RNA interfaces with proteins, ions, and small molecules & nonnatural nucleotides and does not take advantage of multiple processes for speed, but these functionalities are coming soon. E-mail us if you are interested in testing ERRASER2.
ERRASER carries out one-at-a-time remodeling of each nucleotide in the structure, and cannot refine stretches of nucleotides that have major errors. Again, we are working on updates to handle such cases. E-mail us if you have an interesting test case for ERRASER2.
Chou, F.-C., Echols, N., Terwilliger, T.C., and Das, R. (2016)
RNA structure refinement using the ERRASER-Phenix pipeline
Methods in Molecular Biology 1320: 269 - 282. | Paper | Link
Chou, F.-C., Sripakdeevong, P., Dibrov, S.M, Hermann, T., and Das, R. (2013)
Correcting pervasive errors in RNA crystallography through enumerative structure prediction
Nature Methods 10: 74 - 76. | Paper | Link
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