PyMOL4RNA

(See also https://github.com/mmagnus/rna-tools/tree/master/rna_tools/tools/PyMOL4RNA)

Inspect structure

There is new `--inspect` function for rna_pdb_toolsx.py that tells you what are missing atoms in your structure file.

You can run it also from PyMOL, so in here you can see missing atoms directly in PyMOL (the object comes green and the residues missing atoms comes in red).

PyMOL:

inspect <object name>
_images/pymol_inspect.jpeg

and here you can compare the input file vs file after --rpr (of rna_pdb_toolsx.py) to see what was rebuilt (in pink).

_images/pymol_inspect2.jpeg

PyMOL4Spliceosome: all spliceosome structures in one PyMOL session

Download one PyMOL session with structures for each step.

See own project https://github.com/mmagnus/PyMOL4Spliceosome

PyMOL: Color by conservation

Show conserved regions of proteins in PyMOL.

_images/pymol_color_by_conserv.png

See more: https://github.com/mmagnus/rna-tools/tree/master/rna_tools/tools/pymol_color_by_conserv

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

After you install rna-tools, run these two lines your terminal:

$ echo "sys.path.append('`rna_tools_which.py --site`')" >> ~/.pymolrc
$ echo "PyMOL4RNA_PATH='`rna_tools_which.py`/tools/PyMOL4RNA/PyMOL4RNA.py'; cmd.run(PyMOL4RNA_PATH)" >> ~/.pymolrc

so something like this will be added to your ~/.pymolrc:

sys.path.append('/Users/magnus/work/src/rna-tools')
PyMOL4RNA_PATH='/Users/magnus/work/src/rna-tools/rna_tools/tools/PyMOL4RNA/PyMOL4RNA.py'; cmd.run(PyMOL4RNA_PATH)