PyMOL4RNA

PyMOL Drawing

rna_tools.tools.pymol_drawing.pymol_drawing.draw_circle(x, y, z, r=8.0, cr=1.0, cg=0.4, cb=0.8, w=2.0)[source]

Create a CGO circle

PARAMS
x, y, z
X, Y and Z coordinates of the origin
r
Radius of the circle
cr, cg, cb
Color triplet, [r,g,b] where r,g,b are all [0.0,1.0].
w
Line width of the circle
RETURNS
the CGO object (it also loads it into PyMOL, too).
rna_tools.tools.pymol_drawing.pymol_drawing.draw_circle_selection(selName, r=None, cr=1.0, cg=0.4, cb=0.8, w=2.0)[source]

circleSelection – draws a cgo circle around a given selection or object

PARAMS
selName
Name of the thing to encircle.
r
Radius of circle. DEFAULT: This cript automatically defines the radius for you. If you select one atom and the resultant circle is too small, then you can override the script’s calculation of r and specify your own.
cr, cg, cb
red, green and blue coloring, each a value in the range [0.0, 1.0]
RETURNS
The circle object.
rna_tools.tools.pymol_drawing.pymol_drawing.draw_dist(54.729, 28.9375, 41.421, 55.342, 35.3605, 42.745)[source]

https://sourceforge.net/p/pymol/mailman/message/25795427/

rna_tools.tools.pymol_drawing.pymol_drawing.draw_dists(interactions)[source]
rna_tools.tools.pymol_drawing.pymol_drawing.draw_vector(x1, y1, z1, x2, y2, z2)[source]

https://pymolwiki.org/index.php/CGOCylinder

Install PyMOL plugin to view the interactions with PyMOL:

run <path>rna-tools/tools/pymol_drawing/pymol_dists.py

and type:

draw_dists([[29, 41], [7, 66], [28, 42], [51, 63], [50, 64], [2, 71], [5, 68], [3, 70], [31, 39], [4, 69], [6, 67], [12, 23], [52, 62], [30, 40], [49, 65], [27, 43], [11, 24], [1, 72], [10, 25], [15, 48], [53, 61], [19, 56], [13, 22], [36, 37], [18, 19], [22, 46], [35, 73], [32, 38], [9, 13], [19, 20], [18, 20], [54, 60], [9, 23], [34, 35], [36, 38], [53, 54], [20, 56], [9, 12], [26, 44], [18, 55], [54, 61], [32, 36]])
_images/pymol_dists.png

Install

Open your ~/.pymolrc and set up following variables as you need:

# rna-tools
RNA_TOOLS="/Users/magnus/work-src/rna-tools"
EXECUTABLE="/bin/zsh" # set up your shell, usually /bin/bash or /bin/zsh
SOURCE="source ~/.zshrc" # set up the path to the file where you keep your shell variables
CLARNA_RUN="/Users/magnus/work-src/clarna_play/clarna_run.py"  # if you want to run clarna_run.py set up the path
sys.path.append('/Users/magnus/work-src/rna-tools')
run ~/work-src/rna-tools/rna_tools/tools/PyMOL4RNA/PyMOL4RNA.py
run ~/work-src/rna-tools/rna_tools/tools/pymol_drawing/pymol_drawing.py
run ~/work-src/rna-tools/rna_tools/tools/rna_filter/pymol_dists.py

The plugins have been tested with MacPyMOL version 1.7.4.5 Edu.