Quickdisplays

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Type Python Module
Download quickdisplays.py
Author(s) Andreas Warnecke
License BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

The module quickdisplays is a package containing several functions for quick standard displays:

List of functions
Function What it does Usage
disp_list prints a list of functions disp_list
disp_ss secondary structure disp_ss [ selection [, colors [, only ]]]
disp_ball_stick balls and sticks disp_ball_stick [ selection [, hydrogens [, only ]]]
disp_mesh surface mesh disp_mesh [ selection [, color_m [, hydrogens [, only [, limits ]]]]]
disp_surf surface disp_surf [ selection [, color_s [, transparency [, hydrogens [, solvent [, ramp_above [, only [, limits ]]]]]]]]
disp_putty putty b-factor sausage disp_putty [ selection [, limits [, only ]]]
  • Note that each function has an individual help description, callable by entering, e.g.:
help disp_surf


Examples
Quickdisplays disp surf.png
disp_surf
surface
Quickdisplays disp ss.png
disp_ss
secondary structure
Quickdisplays disp putty.png
disp_putty
putty b-factor sausage

The combined displays example was produced like this:

import quickdisplays
fetch 1hpv, async=0

disp_putty all, limits=10
disp_surf color_s=lightblue, transparency=0.8
disp_ss chain B
disp_ball_stick hetatm
util.cbao hetatm
set mesh_mode, 1 # make sure hetams are meshed
set mesh_cutoff, 4.5
disp_mesh resn 478, color_m=green
Quickdisplays disp mesh.png
disp_mesh
mesh
Quickdisplays disp ball stick.png
disp_ball_stick
balls and sticks
Quickdisplays combo.png
combined displays
see example

Some notes on the arguments

  • selection can be used to restrict the display to certain objects or selections, the default is 'all'
  • only can be True or False and will toggle whether the display will be added (show) or replace others (show_as)
  • disp_mesh and disp_surf support the color putty, which will color the object/selection by b-factor
  • limits defines the b-factor color range:
    • a list entry will define absolute values [min;max]
    • a float value will calculate the corresponding percentiles ±value%, default=5
  • setting hydrogens will add hydrogen to the model; if set to =False, hydrogens are removed, if omitted the state of hydogens will be 'as is'
  • colors in disp_ss is flexible:
    • set e.g. three colors, e.g. 'red green blue' for sheets, helices and loops, respectively (cf. example)
    • alternatively certain 'util.' functions can be used (cf. example)
    • setting False once or for individual colors will suppress coloring


Applied example

Enter the following lines one-by-one and observe how the display will be affected

# import function to PyMOL
import quickdisplays

# prep
fetch 1hpv, async=0
bg black
orient
disp_list # list of functions

help disp_ss # check out help
disp_ss
disp_ss only=T
disp_ss colors=smudge orange grey
disp_ss colors=chartreuse False False # False suppresses coloring
disp_ss colors=util.chainbow # You can use util.cbc, util.rainbow, ...

help disp_ball_stick # check out help
disp_ball_stick hetatm
disp_ball_stick all, only=T
util.cbaw
disp_ball_stick hydrogens=1
disp_ball_stick hydrogens=-1
disp_stick_ball # will this work?

help disp_mesh # check out help
disp_mesh
disp_mesh color_m=green, only=False
disp_mesh color_m=green, only=T
disp_ball_stick hetatm
set mesh_skip, 2 # omits lines in mesh
disp_mesh color_m=default, hydrogens=1, only=T
disp_mesh color_m=putty, hydrogens=0, limits=20
disp_mesh color_m=putty, limits=30
disp_mesh color_m=putty, limits=[15,50]

help disp_putty # check out help
disp_putty chain A, only=False, limits=[15,50] #only default is True
disp_putty all, limits=0
disp_putty all, limits=10

help disp_surf # check out help
disp_surf color_s=white, solvent=1
disp_surf color_s=white# solvent=0
disp_surf color_s=lightblue, transparency=0.8


SEE ALSO

Git intro, Displaying Biochemical Properties