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.: