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Job short description (visible in queue):


Basic Inputs



FASTA

Input fasta file of the target sequence (RNA is lowercase!). Format as:
>my_rna A:0-11
gcaugcaagcau
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 auto-DRRAFTER_setup.py 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 auto-DRRAFTER_setup.py 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):