cmuts visualize

Purpose

cmuts visualize may be used to overlay a reactivity profile generated via cmuts onto a 3D RNA structure.

Usage

The general syntax is

cmuts visualize \
  --file "$PROFILES" \
  --dataset "$NAME" \
  --fasta "$FASTA" \
  --cif "$CIF"

and an example can be found under ./examples/visualize.

The FASTA file is necessary to perform alignment of the sequence which was probed against the sequence of the 3D structure, which may be different e.g. due to flanking sequences.

Command Line Options

Core Options

--file : Path to the HDF5 file containing the reactivity data

--dataset : Reactivity dataset name in the HDF5 file

--fasta : Path to .fasta file of the library which was chemically probed

--cif : Path to the .cif structure file (.pdb also works)

--bin : Path to the ChimeraX executable (default: ChimeraX)

Selection Options

--index : Index of the sequence in the FASTA and the reactivity in the HDF5 file (default: 0)

--chain : Color this chain of the structure (default: ALL)

--trim-5p : Trim this many bases from the 5' end of the reactivity data (default: 0)

--trim-3p : Trim this many bases from the 3' end of the reactivity data (default: 0)

Output Options

--color : The ChimeraX color to use for highly reactive bases (default: indianred)

Movies

Once the structure is loaded into ChimeraX, you can record a movie of it rotating by running

movie record
turn y 0.5 720
movie stop
movie encode PATH-TO-MOVIE