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Job short description (visible in queue):

Just specify sequence and dot-bracket secondary structure.

Use [almost] any options available to command line FARFAR2, including local template structures, "general" secondary structure (allowing noncanonical pairs), chemical mapping data, and more.


Sequence

RNA sequence as a single line of text.
:

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. Use . for any regions specified explicitly as starting PDBs, even if those regions are helical.
:

FASTA input

FASTA

Input fasta file of the target sequence (In the FASTA context, in order to represent RNA-protein complexes, RNA is lowercase and protein is uppercase!). Format as: 
>my_rna A:1-12
gcaugcaagcau
If you provide input PDBs, the numbering in those files has to correspond to this fasta file. FASTA input is the only way to supply chemically modified nucleotides; the FARFAR documentation has the full list of well-supported chemically modified nucleotides.
 


Secondary structures (in dot-bracket notation)

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. Use . for any regions specified explicitly as starting PDBs, even if those regions are helical.
 


General secondary structure

Dot-bracket "general" secondary structure of the target (can include noncanonical pairs).
 


Chain connections

Specify sets of residues (as 
SET1 ... SET2 ...
) where there much be at least one base pair between SET1 and SET2, but you don't know where. Especially useful for systems with multiple chains.
:

Noncanonical pairs

Specify individual noncanonical pairs using both residues, the interacting edges (W/H/S for Watson-Crick, Hoogsteen, and sugar, or X for any), and finally the interaction orientation (either C/T for cis/trans or P/A for parallel/antiparallel, or X for any).
:

Constraints

Staged constraints

Apply constraints in stages, over the course of the low-resolution protocol, depending on sequence separation

Constraint file

File specifying energetic restraints following Rosetta's constraint syntax.
For MOHCA-seq constraints, please refer to this example.
 


Constraint weight

Weight for any specified constraints (ignored if set to zero):

PDB Inputs

Input template files

Input PDB file(s) of RNA. (Waters and unrecognized small molecules will NOT be removed)
 


Alignment PDB

PDB file containing part of the target model to which to align the simulation, using 4.0 A RMSD constraints.
 


Native PDB

Ground truth structure of the whole RNA of interest.
 


High Resolution Settings

Minimization

After fragment assembly, run full-atom refinement in a high-resolution scorefunction
Minimization scoring function choices:
Use the original FARFAR scorefunction
Use the most recently published scoring function for FARFAR2 (recommended)
Use the BETA scoring function currently under active evaluation and development (not recommended)

Residues for 'extra' minimization

Residues that can move during minimization even though they were part of a 'fixed' input template. Format as "A:1-3 A:5 B:1-2":

Low Resolution (Fragment Stage) Settings

Fragment set:
Use the ribosome fragments from 1jj2 (FARNA paper)
Use the Rosetta default fragment library (Richardson 2009)
Use the new fragments from the FARFAR2 paper (Das 2018)

Temperature

Monte Carlo simulation temperature. Ignored if left at the default of 2.0.:

Approximate symmetry

Impose a symmetry 'hack'; to model a homodimer duplex, set to 2 and fragment moves to residue 1 will be replicated at residue 1 + len/2 and so on. (For a trimer, set to 3, etc.) Ignored if left at 1.:

Extra fragment samples

Add additional 'fuzzed' fragment samples, chosen from a distribution with this standard deviation in degrees. Ignored if zero.:

Fragment homology exclusion

If there is a provided native structure, ensure that homologous fragments are exclusded from the fragment library to enable rigorous benchmarking
RMSD radius for fragment exclusion:
Sequence match for homology exclusion:
Totally sequence independent; only RMSD criterion applies
6mer fragment sequence must also match up to purine/pyrimidine identity
A 6mer must be identical in sequence to be excluded

Experimental data

Chemical shifts

File specifying RNA chemical shifts, formatted using the STAR2.1 variant described here.
 



# Structures

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