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Andwar at 14:48, 3 December 2014

2014-12-03T14:48:18Z

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Fixing capitalization

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Andwar: /* SEE ALSO */ updated category

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created script page

New page

{{Infobox script-repo
|type = Python Module
|filename = quickdisplays.py
|author = [[User:Andwar|Andreas Warnecke]]
|license = BSD-2-Clause
}}

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

{| class="wikitable"
!colspan="3;"|List of functions
|- style="text-align:center;"
! scope="col"| Function
! scope="col"| What it does
! scope="col"| Usage
|-
! scope="row"| disp_list
| style="text-align:center;"| prints a list of functions
| disp_list
|-
! scope="row"| disp_ss
| style="text-align:center;"| secondary structure
| disp_ss [ selection [, colors [, only ]]]
|-
! scope="row"| disp_ball_stick
| style="text-align:center;"| balls and sticks
|disp_ball_stick [ selection [, hydrogens [, only ]]]
|-
! scope="row"| disp_mesh
| style="text-align:center;"| surface mesh
| disp_mesh [ selection [, color_m [, hydrogens [, only [, limits ]]]]]
|-
! scope="row"| disp_surf
| style="text-align:center;"| surface
| disp_surf [ selection [, color_s [, transparency [, hydrogens [, solvent [, ramp_above [, only [, limits ]]]]]]]]
|-
! scope="row"| disp_putty
| style="text-align:center;"| putty b-factor sausage
| disp_putty [ selection [, limits [, only ]]]
|}

* Note that each function has an '''individual help destription''', callable by entering, e.g.:
help disp_surf
* For instruction on setting up plugin import see [[Git intro]] or [[Plugin manager]]

{| class="wikitable"
!colspan="5;"|Examples
|- style="text-align:center;"
| [[Image:Quickdisplays_disp_surf.png|center|300px]]'''disp_surf''' ''surface''
| [[Image:Quickdisplays_disp_ss.png|center|300px]]'''disp_ss''' ''secondary structure''
| [[Image:Quickdisplays_disp_putty.png|center|300px]]'''disp_putty''' ''putty b-factor sausage''
| colspan="2;" rowspan="2;" style="text-align:left;" |

The ''combined displays'' example was produced like this:
<source lang="python">
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
</source>
|- style="text-align:center;"
| [[Image:Quickdisplays_disp_mesh.png|center|300px]]'''disp_mesh''' ''mesh''
| [[Image:Quickdisplays_disp_ball_stick.png|center|300px]]'''disp_ball_stick''' ''balls and sticks''
| [[Image:Quickdisplays_combo.png|center|300px]]''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
<source lang="python">
# 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
</source>

==SEE ALSO==
[[Git intro]], [[Displaying Biochemical Properties]]

[[Category:Biochemical_Properties]]

@@ Line 40: / Line 40: @@
 |}
-* Note that each function has an '''individual help destription''', callable by entering, e.g.:
+* 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]]

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 [[Git intro]], [[Displaying Biochemical Properties]]
+[[Category:Script_Library]]
 [[Category:Biochemical_Properties]]

Quickdisplays - Revision history

Bell: 1 revision

Andwar at 14:48, 3 December 2014

Bell: 1 revision

Sbliven: Fixing capitalization

Bell: 2 revisions

Andwar: /* SEE ALSO */ updated category

Andwar: created script page