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Job short description (visible in queue):

Basic Inputs


Input fasta file of the target sequence (RNA is lowercase!). Format as:
>my_rna A:0-11
If you provide input PDBs, the numbering in those files has to correspond to this fasta file.

Secondary structure

Dot-bracket secondary structure of the target. Must be the same length, in total number of residues, as the target fasta. May use []{}<> for pseudoknots.

Map-fit structure

The one RNA component that has been fit to the experimental density map.

Other input PDB files

The additional input PDB files that the script generates. You should include a separate PDB file here for every predicted helix in your target RNA.

Optional: Initial structure

Used in the penultimate round of auto-DRRAFTER modeling, this structure gives initial positions for many of the input PDB helices (generally, those regions that are most highly converged) and is generated by the script.

If initial structure is provided: all other input PDBs

If you specify an initial structure above, please provide all the input structures that are not accounted for by the initial structure alignment here.

Optional: Native

A native structure, if one is known. Must match the target fasta in numbering.

Experimental Data Settings

Density map

Map file in .mrc or .ccp4 format. If your map is large (>64MB or so) please gzip it first, as upload will probably otherwise fail.

Density map resolution:

Rather than taking the first map-fit structure as absolutely fixed, allow it to re-dock into the density map.

"Dock chunk" PDB files

RNA components that can dock into density, used in the second-to-last round of autoDRRAFTER modeling.

Job Management Settings

Job prefix

A convenient prefix for your output files. If you intend to use this server multiple times for this round of modeling, evaluating a different helix fit each time, then you may want to specify this as foo_0, foo_1, etc. according to the job setup script.:

Current round

The round number (influences file naming):

This is a "final round" of modeling.

# Structures

The number of structures to generate:

Job Settings

Job Description (for your own records):