RiboKit : RiboVis

Most Useful Commands

• rr(), or render_rna()

Rhiju’s favorite coloring of RNA with 2′ OH as spheres, bases as filled rings, and backbone as cartoon ribbons, rainbow colored from 5′ to 3′. No hydrogens, white background.

• rrs(), or render_rna_sticks()

Rhiju’s favorite coloring of RNA, showing all heavy atoms as sticks – more detail than rr().

• color_by_data( filename [, offset = 0, min = 0, max = 1] )

Read in a text file with rows and color specified residue numbers by scalar values.

125 0.12
126 1.50

Takes advantage of B-factor column and color by temperature function in pymol.

By default, coloring is scaled/offset based on lowest/highest scalar value. To specify the minimum and maximum values for coloring, enter a min and max value as shown above. For normalized chemical mapping reactivities, min = 0 and max = 1~1.5 usually works.

For instructions on coloring 3D models using analyzed reactivity data from HiTRACE, see instructions here.

• rd(), or render_molecules()

Rhiju’s favorite coloring of proteins and generic molecules side chains are all-heavy-atom and colored CPK, backbone is rainbow cartoon from N to C terminus.

• loop_color( start, end, native=None, zoom=False )

Used for rendering protein loop modeling puzzles. White in background, colored red/blue over loop.

• align_all( [ subset=[] ] )

Superimpose all open models onto the first one. This may not work well with selections.

Additional Commands

• rc(), or render_cartoon()

Tube coloring for large RNA comparisons

• sa( [intra=False, rainbow=True] ), or superimpose_all()

Superimpose all open models onto the first one. This may not work well with selections.

Option intra can be set to True to enable intra_fit() first, for working with multi-state (nmr) pdbs. [Thanks to Kyle Beauchamp for this one]

• chainbow()

Run chainbow on all molecules, one by one.

• rx(), or render_x()

Rhiju’s favorite coloring of proteins, more details – no cartoon; heavy backbone. Use for beta peptide visualization.

• rj(), or render_rhiju()

Rhiju’s residue-level favorite coloring of proteins non-polar side chains colored gray.

• rr2(), render_rna2()

Rhiju’s favorite coloring of RNA, showing all heavy atoms as sticks – more detail than rr().

• get_residue_colors( sele )

Get RGB color values associated with a selection. Useful if you want to exactly match coloring of 3D models with coloring in, say, a MATLAB script.

• spr(), or source_pymol_rhiju()

Load up these commands again after, say, an edit.

• rb()

Basic cartoon coloring