PyMOL Wiki - User contributions [en]

Category:Modeling and Editing Structures

2006-12-14T13:42:35Z

Krother:

=Modeling in PyMOL=

==Saving with transformed coordinates==

Here is a simple script that saves the molecule with coordinates from the current orientation.
(invoke it with 'run save_transformed.py' and type the new save_transformed.py command thereafter).
<source lang="python">
# Adds the command save_transformed
# Usage: save_transformed object, file
def save_transformed(object,file):
m = cmd.get_view(0)
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
cmd.transform_object(object,ttt)
cmd.save(file,object)

cmd.extend('save_transformed',save_transformed)
</source>

==Translate or rotate individual objects==
There is a "translate" function similar to "rotate", the docs for these don't exist yet, because the implementation isn't finished. However, feel free to use them in the following forms:

<source lang="python">
translate vector,object-name,state
(vector needs to be something like [x,y,z])

translate [1,0,0],pept

rotate axis,angle,object-name,state
(axis can be either the letter x,y,z or a 3D vector [x,y,z])
rotate x,90,pept
rotate [1,1,1],10,pept
</source>

==Moving one segment relative to the rest==

This means moving two parts of one object into different directions. The easiest way to do this is to split the objects and then use the rotate command.
<source lang="python">
load 1FJ1.pdb

# split PDB file

create anti=(chain F)
create fab=(chain A,B)

# delete original object
delete 1FJ1

# color objects
color green,fab
color pink,anti

# color interface
select inter = (byres ((fab within 5 of anti)\
or (anti within 5 of fab)))

color yellow,inter

# splay apart
orient
origin fab
rotate y,60,fab
origin anti
rotate y,-60, anti

# zoom interface region
zoom inter
show sph,inter
disable inter
</source>

==Split states to objects==
There is also a new command in the 0.95 series:
<source lang="python">
split_states object-name
</source>
which will spread a PDB "biological unit" (or any multi-state object -- including SD files) over a series of independent objects. This makes it possible to interact with such objects more naturally than with "all_states = 1".

==Altering secondary structures==

Examples:
<source lang="python">
alter A/10:34/, ss='H'
alter A/35:40/, ss='L'
alter A/41:60/, ss='S'
</source>

==Altering van der Waals radii==

Example:
<source lang="python">
alter (elem Fe),vdw=1.8
rebuild
</source>
(The value for Fe is wrecked in PyMOL at the moment, so running the above line might be a good idea).

==Altering atom coordinates==

Example:
<source lang="python">
alter_state 1,(pdb1cse),x=x-10.0
</source>
The latter section can contain formulae involving at least the xyz coordinates, lots of constants and the (+-*/) operators.

==Deleting bonds==

Select the bond using Ctrl-right-click, then either
<source lang="python">
unbond pk1,pk2
</source>
or hit Ctrl-D.

==Converting D- to L- amino acids==
The inversion function was changed in version 0.95 to take advantage of multiple picked atoms. To invert a center, Ctrl-middle-click to pick the center atom as pk1 and two stationary atoms as pk2 and pk3. Then type Ctrl-E to invert.

==Adding disulfide bonds==
You can use the [[Cmd bond]] command to attach them:
<source lang="python">
bond 24/sg,26/sg
bond 56/sg,99/sg
unpick
</source>
(unpick will hide the bond baton which gets displayed.)
Additionally, the residue names can be changed for bonded cysteines:
<source lang="python">
alter cys/,name='CYX'
</source>
or for specific residues
<source lang="python">
alter 24+26+56+99/,name='CYX'
</source>

==Adding hydrogen bonds==
See 'displaying biochemical properties'.

==Protonating ligands==
If your ligands come in with valid valencies and formal charges, PyMOL's h_add command can protonate ligands. (NOTE that there is a minor technical hiccup with SD-files which are loaded by default as immutable "discrete" objects.) Suffice it to say that in order to make changes to the chemical structure, an object must be loaded with the "discrete" flag set to zero.
Unfortunately, much of the molecular editing stuff remains to be documented. Here's an example sequence, but I'm not sure it will help to much...as indicated in the manual, this is immature functionality with some major gaps. Attach in particular is very limited...

<source lang="python">
# show valences
set valence=0.05

# load cysteine fragment
fragment cys

# remove hydrogens
remove (hydro)

# edit gamma S
edit cys////sg

# add hydrogen
attach H,1,1

# add planer, trivalent nitrogen onto C terminus
edit cys////C
attach N,3,3

# edit that nitrogen
edit (elem N and neighbor cys////C)

# attach a tetrahedral methyl (note random position)
attach C,4,4

# here's an example of adding a whole residue from the library
edit cys////N
editor.attach_amino_acid("pk1","ace")

# now restore missing hydrogens (note that the names are off...)
h_add
</source>

==Superposition of two molecules==
Using pair_fit requires that you specify a set of paired atoms in each structure. Fortunately, you no longer have to specify each pair separately, so long as the ordering is the same in each selection (almost always true).
<source lang="python">
pair_fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid 10:15 and name P )
</source>

Another example:
<source lang="python">
pair_fit prot1///11-26/CA, prot2///34-49/CA
</source>
would superimpose prot1 on prot2 using C-alphas from residues 11-26 in prot1 and 34-49 in prot2.

==Manual superposition of two molecules==
You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.

Protect one object, deprotect the other, grab the deprotected object and move with Shift-Mouse.
Don't forget to switch to Mouse Editing mode.

==Adding and using your own fragments==
Pymol has some build-in fragments (amino acids and simple functional groups). You can add your own fragments, eg. sugars, in this way:

Create the molecule you want to use as a fragment. Save it as a .pkl file in <pymol_path>/data/chempy/fragments.

How to use the fragment:

Pick the atom (ctrl-middle) where you want to add the fragment. This will usually be a hydrogen atom (which will be removed). Then use the command:

editor.attach_fragment('pk1','my_fragment_name',11,0)

where my_fragment_name is the name of the pkl-file (w/o .pkl extension) and 11 is the number of the connecting (hydrogen) atom in the fragment.
To determine this number, press '[L]abel' -> 'atom identifiers' -> 'index' and choose the hydrogen atom you want.

If you want a hotkey for your fragment, you can probably put it in <pymol_path>/modules/pmg_tk/skins/normal/__init__.py, but I haven't tried this.

[[Category:Advanced Issues|Modeling and Editing Structures]]

PyMOLWiki:Community Portal

2005-03-23T14:05:56Z

Krother:

== CP ==
Look here for ways to get involved in the PyMolWiki!

Editors, you can upload images for your examples and supporting text! Check out [[Special:Upload]].

== Working with Categories ==
To assign pages to categories, use tags at the end of your page containing the category, sub-category and the page name.

Example: There is a page 'Publication Quality Images' in the category 'Advanced Issues' and the sub-category 'Image Manipulation'. It has the tag:
<pre>
[[Category:Advanced_Issues_Image_Manipulation|Publication Quality Images]]
</pre>

== Helping ==
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

=== New! GeShi: Syntax Highlighting for Python & More ===
'''Update''': I have added the option for numbered syntax highlighting and non-numbered.
<pre>
<source lang="python">Non line-numbered code here</source>
</pre>

<pre>
<npython>line-numbered code here</npython>
</pre>

Now with line numbers (or not)!

<npython>
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</npython>

See [http://qbnz.com/highlighter/index.php The Geshi Home Page]

[[User:Tree|Tree]]

Category:Uncategorized

2005-02-23T15:39:42Z

Krother:

==Alter key bindings==
It's not GUI, but you could simply bind a function key such as F1 to a command:
<source lang="python">
cmd.set_key('F1',lambda :cmd.show('sticks'))
</source>

Category:Installation

2005-02-23T15:32:26Z

Krother:

Category:Installation

2005-02-23T15:29:59Z

Krother:

=OS Independent=

[[Category:Installation|OS Independent]]

Key Wait

2005-02-23T15:28:09Z

Krother:

<source lang="python">
#use "spawn spawn_demo.py, local" to invoke this python script from
within pymol
wait=""
i=0
while i < 12 and wait!="x":
cmd.turn("y", 30)
print "Press enter key to continue or x + enter to terminate"
wait=raw_input()
i=i+1
print "Done"
</source>

[[Category:Scripting_Script_Library|Key Wait]]

Color Objects

2005-02-23T15:21:49Z

Krother:

<source lang="python">
#####################################################################
#
# Colour by object
#
#####################################################################

def color_obj(rainbow=0):

"""

AUTHOR

Gareth Stockwell

USAGE

color_obj(rainbow=0)

This function colours each object currently in the PyMOL heirarchy
with a different colour. Colours used are either the 22 named
colours used by PyMOL (in which case the 23rd object, if it exists,
gets the same colour as the first), or are the colours of the rainbow

"""

# Process arguments
rainbow = int(rainbow)

# Get names of all PyMOL objects
obj_list = cmd.get_names('models')

if rainbow:

print "\nColouring objects as rainbow\n"

nobj = len(obj_list)

# Create colours starting at blue(240) to red(0), using intervals
# of 240/(nobj-1)
for j in range(nobj):
hsv = (240-j*240/(nobj-1), 1, 1)
# Convert to RGB
rgb = hsv_to_rgb(hsv)
# Define the new colour
cmd.set_color("col" + str(j), rgb)
print obj_list[j], rgb
# Colour the object
cmd.color("col" + str(j), obj_list[j])

else:

print "\nColouring objects using PyMOL defined colours\n"

# List of available colours
colours = ['red', 'green', 'blue', 'yellow', 'violet', 'cyan', \
'salmon', 'lime', 'pink', 'slate', 'magenta', 'orange', 'marine', \
'olive', 'purple', 'teal', 'forest', 'firebrick', 'chocolate', \
'wheat', 'white', 'grey' ]
ncolours = len(colours)

# Loop over objects
i = 0
for obj in obj_list:
print " ", obj, colours[i]
cmd.color(colours[i], obj)
i = i+1
if(i == ncolours):
i = 0

# HSV to RGB routine taken from Robert L. Campbell's color_b.py script
# See http://biophysics.med.jhmi.edu/rlc/work/pymol/
# Original algorithm from: http://www.cs.rit.edu/~ncs/color/t_convert.html
def hsv_to_rgb(hsv):

h = float(hsv[0])
s = float(hsv[1])
v = float(hsv[2])

if( s == 0 ) :
#achromatic (grey)
r = g = b = v

else:
# sector 0 to 5
h = h/60.
i = int(h)
f = h - i # factorial part of h
#print h,i,f
p = v * ( 1 - s )
q = v * ( 1 - s * f )
t = v * ( 1 - s * ( 1 - f ) )

if i == 0:
(r,g,b) = (v,t,p)
elif i == 1:
(r,g,b) = (q,v,p)
elif i == 2:
(r,g,b) = (p,v,t)
elif i == 3:
(r,g,b) = (p,q,v)
elif i == 4:
(r,g,b) = (t,p,v)
elif i == 5:
(r,g,b) = (v,p,q)
else:
(r,g,b) = (v,v,v)
print "error, i not equal 1-5"

return [r,g,b]

# Add color_obj to the PyMOL command list
cmd.extend("color_obj",color_obj)
</source>

[[Category:Scripting_Script_Library|Color Objects]]

Read PDB-String

2005-02-23T15:18:18Z

Krother:

<source lang="python">
delete all
cmd.read_pdbstr("""HEADER CREATED BY CONVERTPROSPECT 27-JAN-02 2tnf \
REMARK 1 \
ATOM 1 N PRO A 9 1.895 67.213 -38.182 1.00 0.00 N \
ATOM 2 CA PRO A 9 1.703 68.680 -38.402 1.00 0.00 C \
....
ATOM 1153 C GLY A 157 6.927 59.108 -38.901 1.00 6.00 C \
ATOM 1154 O GLY A 157 6.700 59.292 -37.676 1.00 6.00 O \
TER 1155 GLY A 157 \
MASTER \
END \
""","2tnfa")
</source>

[[Category:Scripting_Script_Library|Read PDB-String]]

Get Coordinates II

2005-02-23T15:16:21Z

Krother:

<source lang="python">
from pymol import cmd
from pymol import stored

stored.xyz = []
cmd.iterate_state(1,"pept","stored.xyz.append([x,y,z])")

# at this point, stored.xyz is a native Python array holding
# the coordinates, which you can modify as required

stored.xyz = map(lambda v:[-v[1],v[0],v[2]],stored.xyz)

# and now you can update the internal coordinate sets

cmd.alter_state(1,"pept","(x,y,z)=stored.xyz.pop(0)")
</source>

[[Category:Scripting_Script_Library|Get Coordinates II]]

Get Coordinates I

2005-02-23T15:15:20Z

Krother:

<source lang="python">
from pymol import cmd

model = cmd.get_model("pept")
for a in model.atom:
a.coord=[ -a.coord[1], a.coord[0], a.coord[2]]

cmd.load_model(model,"tmp")
cmd.update("pept","tmp")
cmd.delete("tmp")
</source>

[[Category:Scripting_Script_Library|Get Coordinates I]]

Selection Exists

2005-02-23T15:10:15Z

Krother:

<source lang="python">
#
# The function below will return true if the selection is defined.
#
from pymol import cmd
from types import *

def sele_exists(sele):
sess = cmd.get_session()
for i in sess["names"]:
if type(i) is ListType:
if sele==i[0]:
return 1
return 0
</source>

[[Category:Scripting_Script_Library|Selection Exists]]

Split Movement

2005-02-23T15:03:14Z

Krother:

<source lang="python">
load 1FJ1.pdb

# split PDB file

create anti=(chain F)
create fab=(chain A,B)

# delete original object
delete 1FJ1

# color objects
color green,fab
color pink,anti

# color interface
select inter = (byres ((fab within 5 of anti)\
or (anti within 5 of fab)))

color yellow,inter

# splay apart
orient
origin fab
rotate y,60,fab
origin anti
rotate y,-60, anti

# zoom interface region
zoom inter
show sph,inter
disable inter
</source>

[[Category:Scripting_Script_Library|Split Movement]]

List Selection

2005-02-23T15:01:17Z

Krother:

<source lang="python">
# Using PyMOL commands:
#
list=[]
iterate (name ca),list.append((resi,resn))
print list

[('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), ('LEU',
'6'), ('GLY', '7'), ('GLU', '8'), ('LEU', '9'), ('VAL', '10'), ('TRP', '11'),
('CYS', '12'), ('THR', '13')]

#!/usr/bin/python
#
# as Python script:
#
from pymol import cmd,stored
stored.list=[]
cmd.iterate("(name ca)","stored.list.append((resi,resn))")
print stored.list

[('1', 'ASP'), ('2', 'CYS'), ('3', 'ALA'), ('4', 'TRP'), ('5', 'HIS'), ('6', '
LEU'), ('7', 'GLY'), ('8', 'GLU'), ('9', 'LEU'), ('10', 'VAL'), ('11', 'TRP'),
('12', 'CYS'), ('13', 'THR')]

</source>
[[Category:Scripting_Script_Library|List Selection]]

List Selection

2005-02-23T15:01:01Z

Krother:

List Selection

2005-02-23T15:00:44Z

Krother:

<source lang="python">
# Using PyMOL commands:
#
list=[]
iterate (name ca),list.append((resi,resn))
print list

[('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), ('LEU',
'6'), ('GLY', '7'), ('GLU', '8'), ('LEU', '9'), ('VAL', '10'), ('TRP', '11'),
('CYS', '12'), ('THR', '13')]

#!/usr/bin/python
#
# as Python script:
#
from pymol import cmd,stored
stored.list=[]
cmd.iterate("(name ca)","stored.list.append((resi,resn))")
print stored.list

[('1', 'ASP'), ('2', 'CYS'), ('3', 'ALA'), ('4', 'TRP'), ('5', 'HIS'), ('6', '
LEU'), ('7', 'GLY'), ('8', 'GLU'), ('9', 'LEU'), ('10', 'VAL'), ('11', 'TRP'),
('12', 'CYS'), ('13', 'THR')]

[[Category:Scripting_Script_Library|List Selection]]</source>

CGO Text

2005-02-22T14:32:14Z

Krother:

<source lang="python">
# draw text using cgo
from pymol import cmd
from pymol.cgo import *
from pymol.vfont import plain

cgo = []

axes = [[2.0,0.0,0.0],[0.0,2.0,0.0],[0.0,0.0,2.0]]

pos = [0.0,0.0,0.0]
wire_text(cgo,plain,pos,'Hello World',axes)

pos = [0.0,-3.0,0.0]
cyl_text(cgo,plain,pos,'Hello Universe',0.10,axes=axes)

cmd.set("cgo_line_radius",0.03)
cmd.load_cgo(cgo,'txt')
cmd.zoom("all",2.0)
</source>

Axes

2005-02-22T14:30:40Z

Krother:

<source lang="python">
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</source>

Axes

2005-02-22T14:29:52Z

Krother:

# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')

PyMOLWiki:Community Portal

2005-02-22T14:26:08Z

Krother:

== CP ==
Look here for ways to get involved in the PyMolWiki!

== Helping ==
* A wiki edit/user policy is needed.
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

=== Categories/Content ===
You may now add content to the wiki. This is a semi-structured wiki in that the categories are pseudo-hierarchically linked.
If you feel we're missing a category, please find where it would most logically fit, add it to the main page via the [[Top Level Schema Policy]].

== Section Layout ==
Please see [[:Talk:Main Page|Discussion]] for more thoughts on the site organizaiton.

=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:News Discussion|Discussion]]
## [[:Category:News PyMol Beta|PyMol Beta]]
# [[:Category:Technical Issues|Technical Issues]]
## [[:Category:Technical Issues Installation|Installation]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
# [[:Category:Launching PyMOL|Launching PyMOL]]
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
### [[Linux XFree86 Configuration]] -- wrong place
## [[:Category:Using Pymol Scenes|Scenes]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[:Category:Using Pymol Wizards|Wizards]]
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
# [[:Category:Scripting|Scripting]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
## [[:Category:Scripting Script Library|Script Library]]
# [[:Category:Plugins|Plugins]]
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
## [[:Category:Plugins rtools | rtools]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[:Category:Plugins Others| Others]]
# [[:Category:High-Level Applications|High-Level Applications]]
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[:Category:Third Party Software|Third Party Software]]
## [[:Category:Third Party Software PovRay|PovRay]]
## [[:Category:Third Party Software Movies|Movies]]
## [[:Category:Third Party Software Codecs|Codecs]]
# [[:Category:Python Integration|Python Integration]]
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

=== New! GeShi: Syntax Highlighting for Python & More ===
We now have a syntax highlighter installed. It now supports something like 28 programming languages! When you paste your code simply wrap it in
<language_name> ... code here ... </language_name>.

Here's an example:
<pre>
<python>
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')

<python>
</pre>

gives us the code
<source lang="python">
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</source>

See [http://qbnz.com/highlighter/index.php The Geshi Home Page]

[[User:Tree|Tree]]

PyMOLWiki:Community Portal

2005-02-22T10:22:32Z

Krother: /* Layout Schema */

== CP ==
Look here for ways to get involved in the PyMolWiki!

== Helping ==
* A wiki edit/user policy is needed.
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

=== Categories/Content ===
You may now add content to the wiki. This is a semi-structured wiki in that the categories are pseudo-hierarchically linked.
If you feel we're missing a category, please find where it would most logically fit, add it to the main page via the [[Top Level Schema Policy]].

== Section Layout ==
Please see [[:Talk:Main Page|Discussion]] for more thoughts on the site organizaiton.

=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:News Discussion|Discussion]]
## [[:Category:News PyMol Beta|PyMol Beta]]
# [[:Category:Technical Issues|Technical Issues]]
## [[:Category:Technical Issues Installation|Installation]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
# [[:Category:Launching PyMOL|Launching PyMOL]]
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
### [[Linux XFree86 Configuration]] -- wrong place
## [[:Category:Using Pymol Scenes|Scenes]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[:Category:Using Pymol Wizards|Wizards]]
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
# [[:Category:Scripting|Scripting]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
## [[:Category:Scripting Script Library|Script Library]]
# [[:Category:Plugins|Plugins]]
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
## [[:Category:Plugins rtools | rtools]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[:Category:Plugins Others| Others]]
# [[:Category:High-Level Applications|High-Level Applications]]
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[:Category:Third Party Software|Third Party Software]]
## [[:Category:Third Party Software Movies|Movies]]
## [[:Category:Third Party Software Codecs|Codecs]]
# [[:Category:Python Integration|Python Integration]]
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

=== New! GeShi: Syntax Highlighting for Python & More ===
We now have a syntax highlighter installed. It now supports something like 28 programming languages! When you paste your code simply wrap it in
<language_name> ... code here ... </language_name>.

Here's an example:
<pre>
<python>
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')

<python>
</pre>

gives us the code
<source lang="python">
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</source>

See [http://qbnz.com/highlighter/index.php The Geshi Home Page]

[[User:Tree|Tree]]

Main Page

2005-02-22T09:39:57Z

Krother: Reverted edit of Krother, changed back to last version by Tree

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

We (will) strive to provide
* updates on PyMol
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature rich scripts for general PyMol use

== Links of Interest ==
* Updated! [[PyMolWiki:Community_Portal| How to get involved!]] --read me if you want to add something
* [[:Category:Scripting Script Library| (Nascent) Script Library]] -- add one!
* [[:Category:Commands|PyMol Commands]]
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Main Page

2005-02-22T09:38:59Z

Krother: /* Links of Interest */

Main Page

2005-02-17T08:00:29Z

Krother: /* Proposal for structure */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

== Moving In ==
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.

== Helping ==
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]

== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)
* [[Mouse Controls]]
* [[Command Language]]
* [[Atom Selections]]
* [[Ray-tracing]]
* [[Movies and Animations]]
* [[Cartoon Representations]]
* [[Settings Reference (all settings and what they do)]]
* [[Stereo 3D Display]]
** [[Hardware Options]]
** [[Linux XFree86 Configuration]]
* [[Crystallography Applications]]
** [[Symmetry]]
** [[Electron Density]]
* [[NMR Applications]]
** [[Working with a Family of Structures]]
** [[Superimposition and RMSD]]
** [[NMR Restraints Analysis]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]

* [[Installation]]
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]

* [[Plugins/Modules]]
** [[APBS Plugin]]
** [[rtools Plugin]]

* [[Plugins]]
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]

* [[Structure Alignment]]
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]

* [[Rendering molecules]]
** [[Basics of displaying molecules]]
** [[Coloring molecules]]
** [[Displaying biochemical properties]]

* [[Modeling and editing structures. ]]
** [[Editing atoms]]
** [[Molecular sculpting]]
** [[Homology modeling]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful]]
* [[Creating publication-quality images HOWTO]]

== [[Proposal for structure]] ==
Most of these points fall into some higher category. Here is a proposal how they could be arranged ([[User:Kristian Rother|krother]]):
* I. Technical issues (installation, hardware)
* II. Basic usage (controls, rendering, selections)
* III. Advanced issues (Ray tracing, settings, movies)
* IV. Scripting
* V. Plugins
* VI. High-level applications (Crystallography, NMR)

----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-02-17T07:59:52Z

Krother: /* Initial Wiki Layout Suggestion */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

== Moving In ==
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.

== Helping ==
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]

== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)
* [[Mouse Controls]]
* [[Command Language]]
* [[Atom Selections]]
* [[Ray-tracing]]
* [[Movies and Animations]]
* [[Cartoon Representations]]
* [[Settings Reference (all settings and what they do)]]
* [[Stereo 3D Display]]
** [[Hardware Options]]
** [[Linux XFree86 Configuration]]
* [[Crystallography Applications]]
** [[Symmetry]]
** [[Electron Density]]
* [[NMR Applications]]
** [[Working with a Family of Structures]]
** [[Superimposition and RMSD]]
** [[NMR Restraints Analysis]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]

* [[Installation]]
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]

* [[Plugins/Modules]]
** [[APBS Plugin]]
** [[rtools Plugin]]

* [[Plugins]]
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]

* [[Structure Alignment]]
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]

* [[Rendering molecules]]
** [[Basics of displaying molecules]]
** [[Coloring molecules]]
** [[Displaying biochemical properties]]

* [[Modeling and editing structures. ]]
** [[Editing atoms]]
** [[Molecular sculpting]]
** [[Homology modeling]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful]]
* [[Creating publication-quality images HOWTO]]

== [[Proposal for structure]] ==
Most of these points fall into some higher category. Here is a proposal how they could be arranged [[User:Kristian Rother|krother]]:
* I. Technical issues (installation, hardware)
* II. Basic usage (controls, rendering, selections)
* III. Advanced issues (Ray tracing, settings, movies)
* IV. Scripting
* V. Plugins
* VI. High-level applications (Crystallography, NMR)

----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-02-17T07:59:37Z

Krother: /* Proposal for structure */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

== Moving In ==
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.

== Helping ==
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]

== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)
* [[Mouse Controls]]
* [[Command Language]]
* [[Atom Selections]]
* [[Ray-tracing]]
* [[Movies and Animations]]
* [[Cartoon Representations]]
* [[Settings Reference (all settings and what they do)]]
* [[Stereo 3D Display]]
** [[Hardware Options]]
** [[Linux XFree86 Configuration]]
* [[Crystallography Applications]]
** [[Symmetry]]
** [[Electron Density]]
* [[NMR Applications]]
** [[Working with a Family of Structures]]
** [[Superimposition and RMSD]]
** [[NMR Restraints Analysis]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]

* [[Installation]]
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]

* [[Plugins/Modules]]
** [[APBS Plugin]]
** [[rtools Plugin]]

* [[Plugins]]
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]

* [[Structure Alignment]]
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]

* [[Rendering molecules]]
** [[Basics of displaying molecules]]
** [[Coloring molecules]]
** [[Displaying biochemical properties]]

* [[Modeling and editing structures. ]]
** [[Editing atoms]]
** [[Molecular sculpting]]
** [[Homology modeling]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful]]
* [[Creating publication-quality images HOWTO]]

[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)

== [[Proposal for structure]] ==
Most of these points fall into some higher category. Here is a proposal how they could be arranged [[User:Kristian Rother|krother]]:
* I. Technical issues (installation, hardware)
* II. Basic usage (controls, rendering, selections)
* III. Advanced issues (Ray tracing, settings, movies)
* IV. Scripting
* V. Plugins
* VI. High-level applications (Crystallography, NMR)

----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-02-17T07:58:54Z

Krother: /* Initial Wiki Layout Suggestion */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

== Moving In ==
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.

== Helping ==
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]

== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)
* [[Mouse Controls]]
* [[Command Language]]
* [[Atom Selections]]
* [[Ray-tracing]]
* [[Movies and Animations]]
* [[Cartoon Representations]]
* [[Settings Reference (all settings and what they do)]]
* [[Stereo 3D Display]]
** [[Hardware Options]]
** [[Linux XFree86 Configuration]]
* [[Crystallography Applications]]
** [[Symmetry]]
** [[Electron Density]]
* [[NMR Applications]]
** [[Working with a Family of Structures]]
** [[Superimposition and RMSD]]
** [[NMR Restraints Analysis]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]

* [[Installation]]
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]

* [[Plugins/Modules]]
** [[APBS Plugin]]
** [[rtools Plugin]]

* [[Plugins]]
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]

* [[Structure Alignment]]
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]

* [[Rendering molecules]]
** [[Basics of displaying molecules]]
** [[Coloring molecules]]
** [[Displaying biochemical properties]]

* [[Modeling and editing structures. ]]
** [[Editing atoms]]
** [[Molecular sculpting]]
** [[Homology modeling]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful]]
* [[Creating publication-quality images HOWTO]]

[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)

== [[Proposal for structure]] ==
Most of these points fall into some higher category. Here is a proposal how they could be arranged:
* I. Technical issues (installation, hardware)
* II. Basic usage (controls, rendering, selections)
* III. Advanced issues (Ray tracing, settings, movies)
* IV. Scripting
* V. Plugins
* VI. High-level applications (Crystallography, NMR)

----
[[User:Kristian Rother|krother]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-02-17T07:58:33Z

Krother: /* Proposal for structure */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

== Moving In ==
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.

== Helping ==
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]

== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)
* [[Mouse Controls]]
* [[Command Language]]
* [[Atom Selections]]
* [[Ray-tracing]]
* [[Movies and Animations]]
* [[Cartoon Representations]]
* [[Settings Reference (all settings and what they do)]]
* [[Stereo 3D Display]]
** [[Hardware Options]]
** [[Linux XFree86 Configuration]]
* [[Crystallography Applications]]
** [[Symmetry]]
** [[Electron Density]]
* [[NMR Applications]]
** [[Working with a Family of Structures]]
** [[Superimposition and RMSD]]
** [[NMR Restraints Analysis]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]

* [[Installation]]
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]

* [[Plugins/Modules]]
** [[APBS Plugin]]
** [[rtools Plugin]]

* [[Plugins]]
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]

* [[Structure Alignment]]
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]

* [[Rendering molecules]]
** [[Basics of displaying molecules]]
** [[Coloring molecules]]
** [[Displaying biochemical properties]]

* [[Modeling and editing structures. ]]
** [[Editing atoms]]
** [[Molecular sculpting]]
** [[Homology modeling]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful]]
* [[Creating publication-quality images HOWTO]]

== [[Proposal for structure]] ==
Most of these points fall into some higher category. Here is a proposal how they could be arranged:
* I. Technical issues (installation, hardware)
* II. Basic usage (controls, rendering, selections)
* III. Advanced issues (Ray tracing, settings, movies)
* IV. Scripting
* V. Plugins
* VI. High-level applications (Crystallography, NMR)

----
[[User:Kristian Rother|krother]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-02-17T07:57:34Z

Krother: /* Initial Wiki Layout Suggestion */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

== Moving In ==
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.

== Helping ==
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]

== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)
* [[Mouse Controls]]
* [[Command Language]]
* [[Atom Selections]]
* [[Ray-tracing]]
* [[Movies and Animations]]
* [[Cartoon Representations]]
* [[Settings Reference (all settings and what they do)]]
* [[Stereo 3D Display]]
** [[Hardware Options]]
** [[Linux XFree86 Configuration]]
* [[Crystallography Applications]]
** [[Symmetry]]
** [[Electron Density]]
* [[NMR Applications]]
** [[Working with a Family of Structures]]
** [[Superimposition and RMSD]]
** [[NMR Restraints Analysis]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]

* [[Installation]]
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]

* [[Plugins/Modules]]
** [[APBS Plugin]]
** [[rtools Plugin]]

* [[Plugins]]
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]

* [[Structure Alignment]]
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]

* [[Rendering molecules]]
** [[Basics of displaying molecules]]
** [[Coloring molecules]]
** [[Displaying biochemical properties]]

* [[Modeling and editing structures. ]]
** [[Editing atoms]]
** [[Molecular sculpting]]
** [[Homology modeling]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful]]
* [[Creating publication-quality images HOWTO]]

== [[Proposal for structure]] ==
Most of these points fall into some higher category. Here is a proposal how they could be arranged:
* I. Technical issues (installation, hardware)
* II. Basic usage (controls, rendering, selections)
* III. Advanced issues (Ray tracing, settings, movies)
* IV. Scripting
* V. Plugins
* VI. High-level applications (Crystallography, NMR)

----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-02-17T07:49:33Z

Krother: /* Initial Wiki Layout Suggestion */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

== Moving In ==
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.

== Helping ==
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

We need your help. So join today & happy editing!

[[User:Tree|Tree]]

== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)
* [[Mouse Controls]]
* [[Command Language]]
* [[Atom Selections]]
* [[Ray-tracing]]
* [[Movies and Animations]]
* [[Cartoon Representations]]
* [[Settings Reference (all settings and what they do)]]
* [[Stereo 3D Display]]
** [[Hardware Options]]
** [[Linux XFree86 Configuration]]
* [[Crystallography Applications]]
** [[Symmetry]]
** [[Electron Density]]
* [[NMR Applications]]
** [[Working with a Family of Structures]]
** [[Superimposition and RMSD]]
** [[NMR Restraints Analysis]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]

* [[Installation]]
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]

* [[Plugins/Modules]]
** [[APBS Plugin]]
** [[rtools Plugin]]

* [[Plugins]]
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]

* [[Structure Alignment]]
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]

* [[Rendering molecules]]
** [[Basics of displaying molecules]]
** [[Coloring molecules]]
** [[Displaying biochemical properties]]

* [[Modeling and editing structures. ]]
** [[Editing atoms]]
** [[Molecular sculpting]]
** [[Homology modeling]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful]]
* [[Creating publication-quality images HOWTO]]
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-02-17T07:40:24Z

Krother: /* Initial Wiki Layout Suggestion */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

== Moving In ==
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.

== Helping ==
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

We need your help. So join today & happy editing!

[[User:Tree|Tree]]

== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)
* [[Mouse Controls]]
* [[Command Language]]
* [[Atom Selections]]
* [[Ray-tracing]]
* [[Movies and Animations]]
* [[Cartoon Representations]]
* [[Settings Reference (all settings and what they do)]]
* [[Stereo 3D Display]]
** [[Hardware Options]]
** [[Linux XFree86 Configuration]]
* [[Crystallography Applications]]
** [[Symmetry]]
** [[Electron Density]]
* [[NMR Applications]]
** [[Working with a Family of Structures]]
** [[Superimposition and RMSD]]
** [[NMR Restraints Analysis]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]

* [[Installation]]
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]

* [[Plugins/Modules]]
** [[APBS Plugin]]
** [[rtools Plugin]]

* [[Plugins]]
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]

* [[Structure Alignment]]
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]

* [[Rendering molecules]]
** [[Basics of displaying molecules]]
** [[Coloring molecules]]
** [[Displaying biochemical properties]]

* [[Modeling and editing structures. ]]
** [[Editing atoms]]
** [[Molecular sculpting]]
** [[Homology modeling]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful.]]

----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----