ERRASER Server Documentation

Overview

ERRASER (Enumerative Real-space Refinment ASsisted by Electron-density under Rosetta) is an application for improving RNA crystal structures based on Rosetta. By supplementing the Rosetta RNA scoring function with electron-density restraint, ERRASER can confidently reduce the errors in RNA crystallographic models while retaining a good fit to the diffraction data. Two ERRASER applications are currently available. The standard ERRASER application remodels all the potentially problematic nucleotides in a RNA model in an automatic fashion, and output one final model. The ERRASER single residue rebuilding application apply ERRASER algorithm to a residue specified by user, and return up to 10 top-score models plus the minimized starting model. The first application is useful for automatic improving the entire model globally, and the second application is useful when the user wants to explore all possible alternative conformations for a problematic nucleotide and examine each one manually.

Standard ERRASER application

Tips:

  1. ERRASER only performs Real-Space refinement. User should use PHENIX or other packages for diffraction-based refinement afterwards to obtain the final model.
  2. ERRASER currently does not model the ligands, proteins, and crystal contacts in a structure. Therefore we suggest to fix the position of nucleotides that are in close contact with protein or ligand component. For crystal contacts, one may either fix the position of contacting nucleotides, or include the contacts manually by adding in the crystal packing partners into the starting PDB file and remove them after ERRASER.
  3. The ERRASER application works for RNA structures of all sizes and all resolutions. However we suggest to keep the size below 300 nucleotides, otherwise the computation time may exceed one day.
  4. While one ERRASER run usually corrects most of the errors, it is sometimes beneficial to iterate the ERRASER process. Currently the server is limited to perform one iteration. One may manualy repeat the process by submitting the ERRASER model as the starting model in a new run
  5. For ERRASER refinement of large structure (> 300 nucleotides) or to perform automatic multi-cycle iteration, please download the Rosetta code base and run ERRASER locally on your own computer.

Inputs:

You need to input

  1. Starting pdb file: The pdb file of standard PDB format. No preprocessing is necessary
  2. Electron density map (CCP4): One should supply a 2mFo-DFc map in CCP4 format that covers the entire unit cell. Rfree reflections should be removed in map creation to avoid overfitting. We also suggest one to fill the missing data with calculated data to avoid Fourier truncation error. In PHENIX map calculation utility (GUI), one can use the following options:
    Turn on "Kicked", "Fill missing f obs", and "Exclude free r reflections"
    In "Map region", select "Unit Cell".
  3. Map resolution: Real number, in the unit of Angstrom.
  4. Fixed residue [Optional]: One may fix the position of residues so that they won't move during the ERRASER run (such as residues in close contact with protein/ligand/crystal packing partner; see Tips).
    Example:
    A3-5 A34 B9
    The first letter is the chain name, followed by residue numbers. This example will fix residue 3, 4, 5, 34 in chain A and residue 9 in chain B.

Interpreting Results

  1. The server returns one final model in standard PDB format.
  2. An analysis of the geometric validation results (by MolProbity) and conformational changes between the starting and the final model is also available. The user can examine the changes by ERRASER to ensure there is no significant error introduced by ERRASER. If the user find changes by ERRASER that are unfavorable, the ERRASER single residue rebuilding application can be applied to these problematic sites to obtain several alternative conformation.

ERRASER single residue rebuilding application

Tips:

  1. The application is useful for remodelling residues that are likely to be problematic. Such residues can be known by reading the output of standard ERRASER, by manually inspecting the model, or by MolProbity.
  2. The application only applies to one residue. For rebuilding the entire model automatically, please use the standard ERRASER.

Inputs:

You need to input

  1. Starting pdb file
  2. Electron density map (CCP4)
  3. Map resolution
    See the documentation for standard ERRASER above for detailed explanation.
  4. Rebuild residue: The user need to input the residue to be rebuilt by ERRASER. Both the chain name and the residue number need to be given.
    Format: [chain name][residue number]
    For example, one may input "A23". Here the first letter "A" is the chain name, and "23" is the residue number.

Interpreting Results

  1. The server returns up to 10 final models, sorted by Rosetta score (which includes both the standard physically-realistic score and electron density score), plus the Rosetta-minimized starting model. All outputs are in standard PDB format.
  2. A comparative analysis of the geometric features and the Rosetta score of all the models is given as well. Here the score of the minimized starting model is set to 0 as the baseline. Lower score means the model has better physical energy and/or better fit to the density.

Citations

We'd be grateful if you cite our work in publications that make use of the server:

  1. Chou FC, Sripakdeevong P, Dibrov SM, Hermann T, Das R (2012) Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nature Methods Jan 2013. Link [This is the primary citation for these algorithms]

    2. Additional references of interest:

  2. Sripakdeevong P, Kladwang W, Das R. (2011) An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling, PNAS 108:20573-20578. Link [a new way to solve RNA models, available in the Rosetta codebase]
All papers are available here.

More questions?

We welcome scientific and technical comments on our server. For support please contact us at Rosetta Forums with any comments, questions or concerns.