Quickdisplays

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

• For instruction on setting up plugin import see Git intro or Plugin Manager

Examples
disp_surf surface	disp_ss secondary structure	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
disp_mesh mesh	disp_ball_stick balls and sticks	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