psico.viewing

Viewing and Coloring Stuff

3. 2011 Thomas Holder, MPI for Developmental Biology

License: BSD-2-Clause

Functions

cbm([selection, first_color, _self])	Color by molecule
cbs([selection, first_color, quiet, _self])	Color by segment
get_color_family(color)	API only.
goodsell_lighting(*[, _self])	Mostly flat lighting, similar to the famous illustrations by David Goodsell.
grid_labels([expression, selection, ...])	Create screen stabilized labels per grid cell
nice([selection, simple, _self])	My favourite representation
show_ptm([selection, rep, cys, _self])	Show post-translational modifications.
spectrum_states([selection, ...])	Color each state in a multi-state object different.
spectrumany(expression, color_list[, ...])	Define a color spectrum with as many color-stops as you like (at least 2).

Classes

scene_preserve(*[, _self])

API only.

psico.viewing.cbm(selection='all', first_color=2, *, _self=...)

Color by molecule

Usage

cbm [ selection [, first_color ]]

psico.viewing.cbs(selection='all', first_color=2, quiet=1, *, _self=...)

Color by segment

psico.viewing.get_color_family(color)

API only. Get the colors list from a color submenu (like all “Reds”).

psico.viewing.goodsell_lighting(*, _self=...)

Mostly flat lighting, similar to the famous illustrations by David Goodsell. Works well with spheres representation.

psico.viewing.grid_labels(expression: str = 'model', selection: str = 'enabled', *, subsele: str = 'all', _self=...)

Create screen stabilized labels per grid cell

psico.viewing.nice(selection='(all)', simple=100000.0, *, _self=...)

My favourite representation

Color: by chain (elem C) and by element (others)

Representation: cartoon (polymer), sticks (organic), spheres (inorganic) and nonbonded (solvent)

Usage

nice [ selection ]

class psico.viewing.scene_preserve(*, _self=..., **kwargs)

Bases: object

API only. Context manager to restore the current scene on exit.

psico.viewing.show_ptm(selection='*', *, rep='sticks', cys=True, _self=...)

Show post-translational modifications.

psico.viewing.spectrum_states(selection='all', representations='cartoon ribbon', color_list='blue cyan green yellow orange red', first=1, last=0, quiet=1, *, _self=...)

Color each state in a multi-state object different.

3. 2011 Takanori Nakane and Thomas Holder

Usage

spectrum_states [ selection [, representations [, color_list [, first [, last ]]]]]

Arguments

selection = string: object names (works with complete objects only) {default: all}

representations = string: space separated list of representations {default: cartoon ribbon}

color_list = string: space separated list of colors {default: blue cyan green yellow orange red}

See Also

spectrum, spectrumany

psico.viewing.spectrumany(expression, color_list, selection='(all)', minimum=None, maximum=None, quiet=1, *, _self=...)

Define a color spectrum with as many color-stops as you like (at least 2).

Note: Since PyMOL 1.6, the regular spectrum command also supports arbitrary color lists, so this command is obsolete.

Usage

spectrumany expression, color_list [, selection [, minimum [, maximum ]]]

Arguments

expression = count, resi, b, q, or pc: respectively, atom count, residue index, temperature factor, occupancy, or partial charge {default: count}

color_list = string: Space separated list of colors

… all other arguments like with spectrum command

Example

spectrumany count, forest green yellow white spectrumany b, red yellow white, (polymer), maximum=100.0

See Also

spectrum