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

* '''get_colors''' contains two functions that can be useful when working with colors
** ''get_colors'' : returns all available PyMOL colors
** ''get_random_color'' : returns a random available PyMOL color

* Note that basic colors can be accessed manually without this script from the PyMOL menu under '''Setting''' --> '''Colors...'''
* For instruction on setting up plugin import see [[Git intro]] or [[Plugin manager]]

[[Image:1LSD_random_colors.png|right|300px|1LSD colored randomly by residue]]

==Usage==
get_colors [ selection [, quiet ]]
get_random_color [ selection [, quiet ]]

==Examples==
{|-
||
<source lang="python">
# basic example
get_colors # basic colors
get colors all # larger range with intermediates
</source>

<source lang="python">
#get disco funky
import get_colors
from get_colors import get_colors
from get_colors import get_random_color

cmd.delete('all')
cmd.fetch('1LSD', async=0) # :P
cmd.hide('everything')
cmd.show_as('sticks','not hetatm')
cmd.orient()

python # start a python block
from pymol import stored
stored.atom_list=[]
cmd.iterate('name CA','stored.atom_list.append([model, resi])')
resi_list=["model %s and resi %s"%(value[0],value[1]) for value in stored.atom_list]
for resi in resi_list: cmd.color(get_random_color(),resi)
python end # end python block
cmd.ray()
</source>
||
|}

==SEE ALSO==
* [[Color]]
* [[Get Color Indices]]

[[Category:Script_Library]]
[[Category:UI_Scripts]]

Color

2014-06-10T12:40:16Z

Andwar: /* Getting Atom Colors */ added hint to colors menu and script

'''color''' sets the color of an object or an atom selection to a predefined, named color. For an overview of predifined colors, see [[Color Values]]. For a script that enumerates all the colors see, [[List_Colors]]. If you want to define your own colors, see [[Set_Color]].
===USAGE===
<source lang="python">
color color-name
color color-name, object-name
color color-name, (selection)
</source>

===PYMOL API===
<source lang="python">cmd.color( string color, string selection )</source>

==EXAMPLES==
===Color all carbons yellow===
<source lang="python">color yellow, (name C*)</source>

===Color by Spectrum Example===
Color by spectrum is in the GUI menu but did you realize that the spectrum is not limited to a simple rainbow?
<source lang="python">
spectrum count, palette, object_name
</source>

For available palettes and more details see: [[spectrum]]

===B-Factors===
The command to color a molecule by B-Factors (B Factors) is:
<source lang="python">
spectrum b, selection=SEL
</source>
where '''SEL''' is a valid selection, for example, "protA and n. CA", for protein A's alpha carbons.

For more details see: [[spectrum]]

====Reassigning B-Factors and Coloring====
It is commonplace to replace the B-Factor column of a protein with some other biochemical property at that residue, observed from some calculation or experiment. PyMOL can easily reassign the B-Factors and color them, too. The following example will load a protein, set ALL it's B Factors to "0", read in a list of properties for each alpha carbon in the proteins, assign those new values as the B-Factor values and color by the new values. This example is possible because commands PyMOL does not recognize are passed to the Python interpreter --- a very powerful tool.
<source lang="python">
# load the protein
cmd.load("protA.pdb")

# open the file of new values (just 1 column of numbers, one for each alpha carbon)
inFile = open("newBFactors", 'r')

# create the global, stored array
stored.newB = []

# read the new B factors from file
for line in inFile.readlines(): stored.newB.append( float(line) )

# close the input file
inFile.close()

# clear out the old B Factors
alter protA, b=0.0

# update the B Factors with new properties
alter protA and n. CA, b=stored.newB.pop(0)

# color the protein based on the new B Factors of the alpha carbons
cmd.spectrum("b", "protA and n. CA")
</source>

If you want to save the file with the new B Factor values for each alpha carbon,
<source lang="python">
cmd.save("protA_newBFactors.pdb", "protA")
</source>
or similar is all you need.

A script (data2bfactor.py) that loads data into the B-factor (b) or occupancy (q) columns from an external file can be found in Robert Campbell's PyMOL script repository (http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/)

====Reassigning B-Factors and Coloring - from file ====
<source lang="python">
reinitialize
prot="1XYZ"
cmd.fetch(prot,async=0)

# Set b value to zero
cmd.alter(prot,b=0.0)
cmd.show_as("cartoon",prot)

python
inFile = open("phi_values.txt", 'r')
val_list = []
for line in inFile.readlines()[1:]:
split = line.split()
resn = split[0][0]
resi = split[0][1:-1]
phi_ppm2 = float(split[1])
phi_ppm2_err = float(split[3])
R2_0 = float(split[4])
R2_0_err = float(split[6])
print "Resn=%s Resi=%s, phi_ppm2=%2.2f, phi_ppm2_err=%2.2f, R2_0=%2.2f, R2_0_err=%2.2f"%(resn,resi,phi_ppm2,phi_ppm2_err,R2_0,R2_0_err)

val_list.append(phi_ppm2)
cmd.alter("%s and resi %s and n. CA"%(prot,resi), "b=%s"%phi_ppm2)

python end
minval = min(val_list)
print minval
maxval = max(val_list)
print maxval
cmd.spectrum("b", "blue_white_red", "%s and n. CA"%prot, minimum=0, maximum=maxval)
cmd.ramp_new("ramp_obj", prot, range=[0, minval, maxval], color="[blue, white, red ]")
cmd.save("%s_newBFactors.pdb"%prot, "%s"%prot)
</source>

=== Expanding to Surface ===
See [[Expand_To_Surface]].

If you have run the above code and would like the colors to be shown in the [[Surface]] representation, too, then you need to do the following:
<source lang="python">
# Assumes alpha carbons colored from above.
create ca_obj, your-object-name and name ca
ramp_new ramp_obj, ca_obj, [0, 10], [-1, -1, 0]
set surface_color, ramp_obj, your-object-name
</source>

Thanks to Warren, for this one.

=== Getting Atom Colors ===
<source lang="python">
stored.list = []
iterate all, stored.list.append(color) # use cmd.get_color_tuple(color) to convert color index to RGB values
print stored.list
</source>

Or, you can [[label]] each atom by it's color code:
<source lang="python">
label all, color
</source>

=== What colors does PyMOL currently have? ===
basic colors can be manually accessed and edited from the PyMOL menu under '''Setting''' --> '''Colors...''' 
[[Get_colors]] is a script that allows accessing colors

=== Color States Individually ===
<source lang="python">
fetch 1nmr
set all_states

# the object has 20 states, so we can set separate line colors
# for each state as follows:
for a in range(1,21): cmd.set("line_color","auto","1nmr",a)
</source>
Or, we can do it differently,
<source lang="python">
# start over,
fetch 1nmr

# break apart the object by state
split_states 1nmr

# delete the original
dele 1nmr

# and color by object (carbons only)
util.color_objs("elem c")

# (all atoms)
util.color_objs("all")
</source>

== SEE ALSO ==

* [[Advanced Coloring]]
* [[spectrum]]
* [[Ramp_New]]

[[Category:Objects_and_Selections|Color]]
[[Category:Commands|Color]]
[[Category:States|Coloring states individually]]
[[Category:Coloring|Color]]

Get colors

2014-06-10T12:35:05Z

Andwar: created get_colors page

User:Andwar

2014-06-10T11:52:47Z

Andwar: created user page

Quickdisplays

2014-06-10T11:18:22Z

Andwar: created script 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]]

Valence

2014-06-09T20:42:19Z

Andwar:

== Overview ==
Turning on '''valence''' will enable the display of double bonds. 
Toggling '''valence_mode''' alters the positioning of double bonds (for representation as [[Lines]]) 
'''valence_size''' alters the distance of double bonds. 
Note that bonds can be edited to be delocalized using [[Unbond]] and [[Bond]]. 

== Examples ==
<gallery heights="200px" widths="200px" align="left" perrow="4">
Image:PHE_valence_0.png|set valence, 0 #(no double bonds)
Image:PHE_valence_1_mode_1.png|set valence, 1 set valence_mode, 1 #bonds inside
Image:PHE_valence_1_mode_0.png|set valence, 1 set valence_mode, 0 #bonds centered
Image:PHE_delocalized.png|set valence, 1 #delocalized bonds #(edited: see [[Bond]])
</gallery>

'''valence_size''' alters the distance of double bonds, but behaves slightly different depending on valence_mode 
{| width="45%"
|+ style="font-weight:bold; text-align:center; font-size:100%;" | valence_size
! valence_size with valence_mode 1 inside !! valence_size with valence_mode 0 centered
|-
||[[File:valence_size_mode1.gif]] || [[File:valence_size_mode0.gif]]
|}

== Syntax ==
<source lang="python">
set valence, 0 # off
set valence, 1 # on

set valence_mode, 0 # centered
set valence_mode, 1 # inside

set valence_size, 0.1 # default: 0.06 # range 0 - ~0.5

# Editing bonds:
# In editing mode: select the bond using Ctrl-right-click, then enter:
unbond pk1,pk2
bond pk1,pk2,4
# 1: single bond, 2: double bond, 3:triple bond, 4:delocalized
</source>

==Automatic editing of bonds==
[[Format_bonds]] is a script that automatically formats valence in amino acids.

==SEE ALSO==
[[Bond]], [[Unbond]]

[[Category:Settings|Valence]]

Plugin Manager

2014-06-06T22:50:30Z

Andwar: corrected path for windows

Newer versions of PyMOL come with a '''Plugin Manager''', which can be used to load plugins such as those in the [https://github.com/Pymol-Scripts/Pymol-script-repo# PyMOL Script Repo]. 

=Manual Setup=
In the PyMOL menu naviagte to '''Plugins''' > '''Plugin Manager''' 
Here you can manually add directories or scripts that will be loaded upon startup. 
Older versions have a basic version of this manager: '''Plugin''' > '''Manage Plugins''', however, here the scripts need to be added individually. 

=Scripted setup during PyMOL launching=
===Creating run_on_startup.py===
'''run_on_startup.py''' can easily be created using a text editor such as notepad. 

The '''run_on_startup.py''' is handled similar to [[Pymolrc|pymolrc]] files and is executed every time PyMOL launches. 
An important distinction is that '''run_on_startup.py''' is executed before the [[Pymolrc|pymolrc]] files and is purely written in python. 
The recommended location of '''run_on_startup.py''' is the PyMOL home directory (PYMOL_PATH, e.g. something like 'C:\Program Files \PyMOL\'). 
An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory). 

<syntaxhighlight lang="python">
#this can be copy-pasted to create run_on_startup.py in the home directory

# Add paths to sys.path so PyMOL can find modules and scripts
import sys
import os

pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make setting changes to Plugin Manager
try: # in case the PyMOL is older and doe not have the module pymol.plugins
import pymol.plugins

#THIS IS WHERE THE PATH IS ADDED TO INITIALIZE PLUGINS USING THE PLUGIN MANAGER
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])

pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}
# This can be used to trace if PyMOL executed the file correctly
print 'Loaded run_on_stratup.py'
except:
print 'NB! Plugin Manager not present!'
</syntaxhighlight>
Note that this block will also add the '''Pymol-script-repo''' and the subfolder '''Pymol-script-repo/modules''' to PyMOL's search path. 
This is something that is required in earlier PyMOL version to allow import of scripts. Thus this version of '''run_on_startup.py''' can be used for older versions, too. 
Note that the settings specific for the ''new'' version of the '''Plugin Manager''' will not have an effect. 

===What if the 'Pymol-script-repo' is not in the PyMOL directory?===
If the '''Pymol-script-repo''' is located somewhere else the first section of the '''run_on_startup.py''' file will be different. 
E.g. in the USER directory:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

E.g. in any other path:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.realpath('D:/MY/RANDOM/PATH/TO/Pymol-script-repo') # Adjust this line
# Note the slash ('/') instead of backslash ('\'), beware Windows users!

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

===Appending additional paths to the Plugin Manager===
Should your scripts be located in several alternative locations, it is possible to append additional directories to the '''Plugin Manager'''. 
In the example below, a directory called 'plugins_private', which is located in the PyMOL directory, is added to the Plugin Manger. 
Should the folder be somewhere else the example below can be adjusted as outlined above. 
<syntaxhighlight lang="python">
#copy paste into PyMOL's command line or into the pymolrc

python
import os
import sys
import pymol.plugins # Note that this requires the 'new' Plugin Manager

PRIVATE_PATH=os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'plugins_private'))
startupdirectories=list(pymol.plugins.get_startup_path(True))
if PRIVATE_PATH not in startupdirectories:
startupdirectories.append(PRIVATE_PATH)
if PRIVATE_PATH not in sys.path:
sys.path.append(PRIVATE_PATH)
pymol.plugins.set_startup_path(startupdirectories)
python end
</syntaxhighlight>

Note that the '''Plugin Manager''' supports loading entire folders with scripts ('modules'). 
If you have such a folder, make sure it contains a file called '__init__.py', which can be empty.

=If you don't have a Plugin Manager=
If you are running an older PyMOL without '''Plugin Manager''' you can either upgrade to the newest version or load plugins the traditional way. 
For detailed instructions see: [[Git install scripts]] 
Essentially, make sure that the folder is added to PyMOL's search paths.
<syntaxhighlight lang="python">
import sys
import os
pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
sys.path.append(pymol_git)
</syntaxhighlight>
Import a plugin manually:
<syntaxhighlight lang="python">
# EXAMPLE
delete all
frag LYS
cgo_arrow name N, name O # will not work if 'cgo_arrow' is not loaded

import cgo_arrow # PyMOL will look for this file and load it
cgo_arrow name N, name O # should work if it is loaded
</syntaxhighlight>

=SEE ALSO=
[[Git install scripts]]

[[Category:Launching]]

Plugin manager

2014-06-06T22:50:30Z

Andwar: corrected path for windows

Plugin Manager

2014-06-06T19:14:11Z

Andwar: some editing pointing out differences to the old plugin management

Newer versions of PyMOL come with a '''Plugin Manager''', which can be used to load plugins such as those in the [https://github.com/Pymol-Scripts/Pymol-script-repo# PyMOL Script Repo]. 

=Manual Setup=
In the PyMOL menu naviagte to '''Plugins''' > '''Plugin Manager''' 
Here you can manually add directories or scripts that will be loaded upon startup. 
Older versions have a basic version of this manager: '''Plugin''' > '''Manage Plugins''', however, here the scripts need to be added individually. 

=Scripted setup during PyMOL launching=
===Creating run_on_startup.py===
'''run_on_startup.py''' can easily be created using a text editor such as notepad. 

The '''run_on_startup.py''' is handled similar to [[Pymolrc|pymolrc]] files and is executed every time PyMOL launches. 
An important distinction is that '''run_on_startup.py''' is executed before the [[Pymolrc|pymolrc]] files and is purely written in python. 
The recommended location of '''run_on_startup.py''' is the PyMOL home directory (PYMOL_PATH, e.g. something like 'C:\Program Files \PyMOL\'). 
An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory). 

<syntaxhighlight lang="python">
#this can be copy-pasted to create run_on_startup.py in the home directory

# Add paths to sys.path so PyMOL can find modules and scripts
import sys
import os

pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make setting changes to Plugin Manager
try: # in case the PyMOL is older and doe not have the module pymol.plugins
import pymol.plugins

#THIS IS WHERE THE PATH IS ADDED TO INITIALIZE PLUGINS USING THE PLUGIN MANAGER
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])

pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}
# This can be used to trace if PyMOL executed the file correctly
print 'Loaded run_on_stratup.py'
except:
print 'NB! Plugin Manager not present!'
</syntaxhighlight>
Note that this block will also add the '''Pymol-script-repo''' and the subfolder '''Pymol-script-repo/modules''' to PyMOL's search path. 
This is something that is required in earlier PyMOL version to allow import of scripts. Thus this version of '''run_on_startup.py''' can be used for older versions, too. 
Note that the settings specific for the ''new'' version of the '''Plugin Manager''' will not have an effect. 

===What if the 'Pymol-script-repo' is not in the PyMOL directory?===
If the '''Pymol-script-repo''' is located somewhere else the first section of the '''run_on_startup.py''' file will be different. 
E.g. in the USER directory:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

E.g. in any other path:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.realpath('D:\MY\RANDOM\PATH\TO\Pymol-script-repo') # Adjust this line
# Note the '\' instead of '/', beware Windows users!

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

===Appending additional paths to the Plugin Manager===
Should your scripts be located in several alternative locations, it is possible to append additional directories to the '''Plugin Manager'''. 
In the example below, a directory called 'plugins_private', which is located in the PyMOL directory, is added to the Plugin Manger. 
Should the folder be somewhere else the example below can be adjusted as outlined above. 
<syntaxhighlight lang="python">
#copy paste into PyMOL's command line or into the pymolrc

python
import os
import sys
import pymol.plugins # Note that this requires the 'new' Plugin Manager

PRIVATE_PATH=os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'plugins_private'))
startupdirectories=list(pymol.plugins.get_startup_path(True))
if PRIVATE_PATH not in startupdirectories:
startupdirectories.append(PRIVATE_PATH)
if PRIVATE_PATH not in sys.path:
sys.path.append(PRIVATE_PATH)
pymol.plugins.set_startup_path(startupdirectories)
python end
</syntaxhighlight>

Note that the '''Plugin Manager''' supports loading entire folders with scripts ('modules'). 
If you have such a folder, make sure it contains a file called '__init__.py', which can be empty.

=If you don't have a Plugin Manager=
If you are running an older PyMOL without '''Plugin Manager''' you can either upgrade to the newest version or load plugins the traditional way. 
For detailed instructions see: [[Git install scripts]] 
Essentially, make sure that the folder is added to PyMOL's search paths.
<syntaxhighlight lang="python">
import sys
import os
pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
sys.path.append(pymol_git)
</syntaxhighlight>
Import a plugin manually:
<syntaxhighlight lang="python">
# EXAMPLE
delete all
frag LYS
cgo_arrow name N, name O # will not work if 'cgo_arrow' is not loaded

import cgo_arrow # PyMOL will look for this file and load it
cgo_arrow name N, name O # should work if it is loaded
</syntaxhighlight>

=SEE ALSO=
[[Git install scripts]]

[[Category:Launching]]

Plugin manager

2014-06-06T19:14:11Z

Andwar: some editing pointing out differences to the old plugin management

Newer versions of PyMOL come with a '''Plugin Manager''', which can be used to load plugins such as those in the [https://github.com/Pymol-Scripts/Pymol-script-repo# PyMOL Script Repo]. 

=Manual Setup=
In the PyMOL menu naviagte to '''Plugins''' > '''Plugin Manager''' 
Here you can manually add directories or scripts that will be loaded upon startup. 
Older versions have a basic version of this manager: '''Plugin''' > '''Manage Plugins''', however, here the scripts need to be added individually. 

=Scripted setup during PyMOL launching=
===Creating run_on_startup.py===
'''run_on_startup.py''' can easily be created using a text editor such as notepad. 

The '''run_on_startup.py''' is handled similar to [[Pymolrc|pymolrc]] files and is executed every time PyMOL launches. 
An important distinction is that '''run_on_startup.py''' is executed before the [[Pymolrc|pymolrc]] files and is purely written in python. 
The recommended location of '''run_on_startup.py''' is the PyMOL home directory (PYMOL_PATH, e.g. something like 'C:\Program Files \PyMOL\'). 
An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory). 

<syntaxhighlight lang="python">
#this can be copy-pasted to create run_on_startup.py in the home directory

# Add paths to sys.path so PyMOL can find modules and scripts
import sys
import os

pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make setting changes to Plugin Manager
try: # in case the PyMOL is older and doe not have the module pymol.plugins
import pymol.plugins

#THIS IS WHERE THE PATH IS ADDED TO INITIALIZE PLUGINS USING THE PLUGIN MANAGER
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])

pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}
# This can be used to trace if PyMOL executed the file correctly
print 'Loaded run_on_stratup.py'
except:
print 'NB! Plugin Manager not present!'
</syntaxhighlight>
Note that this block will also add the '''Pymol-script-repo''' and the subfolder '''Pymol-script-repo/modules''' to PyMOL's search path. 
This is something that is required in earlier PyMOL version to allow import of scripts. Thus this version of '''run_on_startup.py''' can be used for older versions, too. 
Note that the settings specific for the ''new'' version of the '''Plugin Manager''' will not have an effect. 

===What if the 'Pymol-script-repo' is not in the PyMOL directory?===
If the '''Pymol-script-repo''' is located somewhere else the first section of the '''run_on_startup.py''' file will be different. 
E.g. in the USER directory:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

E.g. in any other path:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.realpath('D:\MY\RANDOM\PATH\TO\Pymol-script-repo') # Adjust this line
# Note the '\' instead of '/', beware Windows users!

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

===Appending additional paths to the Plugin Manager===
Should your scripts be located in several alternative locations, it is possible to append additional directories to the '''Plugin Manager'''. 
In the example below, a directory called 'plugins_private', which is located in the PyMOL directory, is added to the Plugin Manger. 
Should the folder be somewhere else the example below can be adjusted as outlined above. 
<syntaxhighlight lang="python">
#copy paste into PyMOL's command line or into the pymolrc

python
import os
import sys
import pymol.plugins # Note that this requires the 'new' Plugin Manager

PRIVATE_PATH=os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'plugins_private'))
startupdirectories=list(pymol.plugins.get_startup_path(True))
if PRIVATE_PATH not in startupdirectories:
startupdirectories.append(PRIVATE_PATH)
if PRIVATE_PATH not in sys.path:
sys.path.append(PRIVATE_PATH)
pymol.plugins.set_startup_path(startupdirectories)
python end
</syntaxhighlight>

Note that the '''Plugin Manager''' supports loading entire folders with scripts ('modules'). 
If you have such a folder, make sure it contains a file called '__init__.py', which can be empty.

=If you don't have a Plugin Manager=
If you are running an older PyMOL without '''Plugin Manager''' you can either upgrade to the newest version or load plugins the traditional way. 
For detailed instructions see: [[Git install scripts]] 
Essentially, make sure that the folder is added to PyMOL's search paths.
<syntaxhighlight lang="python">
import sys
import os
pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
sys.path.append(pymol_git)
</syntaxhighlight>
Import a plugin manually:
<syntaxhighlight lang="python">
# EXAMPLE
delete all
frag LYS
cgo_arrow name N, name O # will not work if 'cgo_arrow' is not loaded

import cgo_arrow # PyMOL will look for this file and load it
cgo_arrow name N, name O # should work if it is loaded
</syntaxhighlight>

=SEE ALSO=
[[Git install scripts]]

[[Category:Launching]]

Plugin Manager

2014-06-06T17:53:45Z

Andwar: links to pymolrc page

Newer versions of PyMOL come with a '''Plugin Manager''', which can be used to load plugins such as the [https://github.com/Pymol-Scripts/Pymol-script-repo# PyMOL Script Repo].

=Manual Setup=
In the PyMOL menu naviagte to '''Plugins''' > '''Plugin Manager''' 
Here you can manually add directories or scripts that will be loaded upon startup.

=Scripted setup during PyMOL launching=
===Creating run_on_startup.py===
'''run_on_startup.py''' can easily be created using a text editor such as notepad. 

The '''run_on_startup.py''' is handled similar to [[Pymolrc|pymolrc]] files and is executed every time PyMOL launches. 
An important distinction is that '''run_on_startup.py''' is executed before the [[Pymolrc|pymolrc]] files and is purely written in python. 
The recommended location of '''run_on_startup.py''' is the PyMOL home directory (PYMOL_PATH, e.g. something like 'C:\Program Files \PyMOL\'). 
An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory).

<syntaxhighlight lang="python">
#this can be copy-pasted to create run_on_startup.py in the home directory

# Add paths to sys.path so PyMOL can find modules and scripts
import sys
import os

pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make setting changes to Plugin Manager
import pymol.plugins

#THIS IS WHERE THE PATH IS ADDED TO INITIALIZE PLUGINS USING THE PLUGIN MANAGER
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])

pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}

# This can be used to trace if PyMOL executed the file correctly. Otherwise remove this part
print 'Loaded run_on_stratup.py'
</syntaxhighlight>

If the '''Pymol-script-repo''' is located somewhere else the first section of the file will be different. 
E.g. in the USER directory:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

E.g. in any other path:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.realpath('D:\MY\RANDOM\PATH\TO\Pymol-script-repo') # Adjust this line
# Note the '\' instead of '/', beware Windows users!

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

===Appending additional paths to the Plugin Manager===
Should your scripts be located in several alternative locations, it is possible to append additional directories to the '''Plugin Manager'''. 
In the example below, a directory called 'plugins_private', which is located in the PyMOL directory, is added to the Plugin Manger. 
Should the folder be somewhere else the example below can be adjusted as outlined above. 
<syntaxhighlight lang="python">
#copy paste into PyMOL's command line or into the pymolrc

python
import os
import sys
import pymol.plugins

PRIVATE_PATH=os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'plugins_private'))
startupdirectories=list(pymol.plugins.get_startup_path(True))
if PRIVATE_PATH not in startupdirectories:
startupdirectories.append(PRIVATE_PATH)
if PRIVATE_PATH not in sys.path:
sys.path.append(PRIVATE_PATH)
pymol.plugins.set_startup_path(startupdirectories)
python end
</syntaxhighlight>

Note that the '''Plugin Manager''' supports loading entire folders with scripts ('modules'). 
If you have such a folder, make sure it contains a file called '__init__.py', which can be empty.

=If you don't have a Plugin Manager=
If you are running an older PyMOL without '''Plugin Manager''' you can either upgrade to the newest version or load plugins the traditional way. 
For detailed instructions see: [[Git install scripts]] 
Essentially, make sure that the folder is added to PyMOL's search paths.
<syntaxhighlight lang="python">
import sys
import os
pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
sys.path.append(pymol_git)
</syntaxhighlight>
Import a plugin manually:
<syntaxhighlight lang="python">
# EXAMPLE
delete all
frag LYS
cgo_arrow name N, name O # will not work if 'cgo_arrow' is not loaded

import cgo_arrow # PyMOL will look for this file and load it
cgo_arrow name N, name O # should work if it is loaded
</syntaxhighlight>

=SEE ALSO=
[[Git install scripts]]

[[Category:Launching]]

2014-05-29T20:51:50Z

Andwar:

== Overview ==
Turning on '''valence''' will enable the display of double bonds. 
Toggling '''valence_mode''' alters the positioning of double bonds (for representation as [[Lines]]) 
Note that bonds can be edited to be delocalized using [[Unond]] and [[Bond]].

== Examples ==
<gallery heights="200px" widths="200px" align="left" perrow="4">
Image:PHE_valence_0.png|set valence, 0 #(no double bonds)
Image:PHE_valence_1_mode_1.png|set valence, 1 set valence_mode, 1 #bonds inside
Image:PHE_valence_1_mode_0.png|set valence, 1 set valence_mode, 0 #bonds centered
Image:PHE_delocalized.png|set valence, 1 #delocalized bonds #(edited: see [[Bond]])
</gallery>

== Syntax ==
<source lang="python">
set valence, 0 # off
set valence, 1 # on

set valence_mode, 0 # centered
set valence_mode, 1 # inside

# In editing mode:
# select the bond using Ctrl-right-click, then enter:
unbond pk1,pk2
bond pk1,pk2,4
# 1: single bond, 2: double bond, 3:triple bond, 4:delocalized
</source>

=SEE ALSO=
[[Bond]], [[Unond]]

[[Category:Settings|Valence]]

Valence

2014-05-29T20:49:59Z

Andwar:

== Overview ==
Turning on '''valence''' will enable the display of double bonds. 
Toggling '''valence_mode''' alters the positioning of double bonds (for representation as [[Lines]]) 
Note that bonds can be edited to be delocalized using [[Unond]] and [[Bond]].

== Examples ==
<gallery heights="200px" widths="200px" align="left" perrow="4">
Image:PHE_valence_0.png|set valence, 0 #(no double bonds)
Image:PHE_valence_1_mode_1.png|set valence, 1 set valence_mode, 1 #bonds inside
Image:PHE_valence_1_mode_0.png|set valence, 1 set valence_mode, 0 #bonds centered
Image:PHE_delocalized.png|set valence, 1 #delocalized bonds #(edited: see [[Bond]])
</gallery>

== Syntax ==
<source lang="python">
set valence, 0 # off
set valence, 1 # on

set valence_mode, 0 # centered
set valence_mode, 1 # inside

# In editing mode:
# select the bond using Ctrl-right-click, then enter:
unbond pk1,pk2
bond pk1,pk2,4
# 1: single bond, 2: double bond, triple bond, 4:delocalized
</source>

=SEE ALSO=
[[Bond]], [[Unond]]

[[Category:Settings|Valence]]

Hash max

2014-02-18T13:52:12Z

Andwar:

== Overview ==
[[hash_max]] sets how much memory PyMOL uses when ray tracing.
Higher values will enable PyMOL to ray trace more quickly, provided you can secure the necessary memory. Thus for large scenes, it can be useful to increase this value. Simpler scenes probably don't need it. If '''hash_max''' is set too high, then PyMOL can (and will) crash when it attempts to use more memory than available.
Likewise, '''hash_max''' can be used to limit the use of memory to avoid crashes at the expense of increased computing time.

== Syntax ==
<source lang="python">
set hash_max, int
</source>
where '''int''' is a positive integer. The default value is 100.

== Example ==
<source lang="python">
set hash_max, 200
</source>

== See Also ==
[[ray]], [[png]], [[draw]]

[[Category:Settings|Hash_Max]]
[[Category:Performance]]