Create

2013-02-11T23:42:50Z

RuneKidmose:

'''create''' creates a new molecule object from a selection. It can also be used to create states in an existing object.
'''NOTE''': this command has not yet been throughly tested.

===USAGE===
<source lang="python">
create name, (selection) [,source_state [,target_state ] ]
create name = (selection) [,source_state [,target_state ] ] # (DEPRECATED)
</source>

* name = object to create (or modify)
* selection = atoms to include in the new object
* source_state (default: 0 - copy all states)
* target_state (default: 0)

===PYMOL API===
<source lang="python">
cmd.create(string name, string selection, int state, int target_state,int discrete)
</source>

===NOTES===
If the source and target states are zero (default), all states will be copied. Otherwise, only the indicated states will be copied.

===SEE ALSO===
[[Cmd load|load]], [[Cmd copy|copy]], [[Extract]]

=== User Comments/Examples ===

===EXAMPLES===
<source lang="python">
# merging two multi-state objects with the create command
# obj1 has 25 states and obj2 has 40 states

load multi_state_obj1, obj1
load multi_state_obj2, obj2

# merge the two multi-state objects back to back into obj3
# 0 indicates every states from obj1 should be included
# 1 indicates that the first state of obj3 is the first state from obj1 etc.

create obj3, obj1, 0, 1

# as obj1 has 25 states, the first state of obj2 must be state 26 to create a multi-state object of obj1 and obj2 back-to-back
# 26 indicates that the 26th state of obj3 is state nr. 1 of obj2 etc.

create obj3, obj2, 0, 26

# Obj3 now has 65 states (25 from obj1 and 40 from obj2)
# save obj3 as a multi-state pdb file
# use state=0 to get all states into one pdb file

save obj3.pdb, obj3, state=0
</source>

[[Category:Commands|Create]]
[[Category:States|Create]]
[[Category:Editing Module|Create]]

Advanced Coloring

2011-12-18T19:17:31Z

RuneKidmose: /* Coloring by atom type */

=Coloring Molecules=

==Basic Coloring==
Any molecule in PyMOL can be assigned a color using the small rightmost buttons in the object list (in the upper right part of the main GUI window. The [[Color]] command will do the same.

PyMOL has a predefined set of colors that can be edited in the ''Settings->Colors'' menu.
Alternatively, you can use the [[Set_Color]] command.

==Coloring secondary structures==
To assign helices, sheets and loops individual colors, do:
<source lang="python">
color red, ss h
color yellow, ss s
color green, ss l+''
</source>

When the colour bleeds from the ends of helices and sheets into loops, do:
<source lang="python">
set cartoon_discrete_colors, 1
</source>
Or activate ''Cartoon -> Discrete Colors'' in the GUI menu.

==Coloring by atom type==
The util.cba* ("Color By Atom") commands color atoms according to type: oxygen in red, nitrogen in blue, hydrogen in white. Carbon will get a different colors, depending on the command:
{|
! command
! carbon color
|-
| util.cba'''g'''
| green
|-
| util.cba'''c'''
| cyan
|-
| util.cba'''m'''
| light magenta
|-
| util.cba'''y'''
| yellow
|-
| util.cba'''s'''
| salmon
|-
| util.cba'''w'''
| white/grey
|-
| util.cba'''b'''
| slate
|-
| util.cba'''o'''
| bright orange
|-
| util.cba'''p'''
| purple
|-
| util.cba'''k'''
| pink
|}
For instance:
<source lang="python">
util.cbay three
</source>
will color the object ''three'' by atom type, with the carbon atoms in yellow.

The util.cnc command will color all the atoms according to type, as in the util.cba* commands stated above, except for the C-atoms.

For instance:
<source lang="python">
util.cnc three
</source>
will color the object ''three'' by atom type, but leave the color of the C-atom unaltered.

==CMYK-safe Colors==
There are two distinct color spaces on computers: RGB (red-green-blue), which is for screens, and CMYK (cyan-magenta-yellow-black), which is for printing.
Some RGB triplets do not have equivalents in CMYK space. As a result, a figure that looks great on a screen can come out with unpredictable colors when printed.

Most applications do a good job with RGB-to-CMYK conversions for photos, but do not do such a good job with graphics that use pure primary colors. For example, reds are generally OK, but pure blues and greens do not translate very well.

Here are some RGB values that are within the CMYK gamut (i.e. are "CMYK-safe"):
<source lang="python">
#optimized rgb values for cmyk output:
set_color dblue= [0.05 , 0.19 , 0.57]
set_color blue= [0.02 , 0.50 , 0.72]
set_color mblue= [0.5 , 0.7 , 0.9 ]
set_color lblue= [0.86 , 1.00 , 1.00]

set_color green= [0.00 , 0.53 , 0.22]
set_color lgreen=[0.50 , 0.78 , 0.50]
set_color yellow=[0.95 , 0.78 , 0.00]
set_color orange=[1.00 , 0.40 , 0.0 ]

# these are trivial
set_color red= [1.00 , 0.00 , 0.00]
set_color mred= [1.00 , 0.40 , 0.40]
set_color lred= [1.00 , 0.80 , 0.80]
set_color vlred= [1.00 , 0.90 , 0.90]
set_color white= [1.00 , 1.00 , 1.00]
set_color vlgray=[0.95 , 0.95 , 0.95]
set_color lgray= [0.90 , 0.90 , 0.90]
set_color gray= [0.70 , 0.70 , 0.70]
set_color dgray= [0.50 , 0.50 , 0.50]
set_color vdgray=[0.30 , 0.30 , 0.30]
set_color black= [0.00 , 0.00 , 0.00]
##
</source>

Note that there are default atom colors such as "carbon", "nitrogen", "oxygen", "hydrogen", "sulfur", etc. which should also be redefined:
<source lang="python">
set_color carbon= [0.00 , 0.53 , 0.22]
etc.
</source>

==Coloring with 'chainbows' from a script==
The chainbow function can be invoked by:
<source lang="python">
util.chainbow("object-name")
</source>

==Assign color by B-factor==
B-factor coloring can be done with the [[spectrum]] command. Example:

spectrum b, blue_white_red, minimum=20, maximum=50
as cartoon
cartoon putty

= See Also =
[[Color]], [[Spectrum]]

==Creating a Color bar==
To show a vertical/horizontal color bar indiacting the b-factor variation, use the script pseudobar.pml on the structure pseudobar.pdb, or do the following:
# Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Be sure that CA's are separated by a contant value, say 5 Angstroem.
# Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks).

Also, see the newly created [[spectrumbar]] script!

==Coloring insides and outsides of helices differently==
The inside of helices can be adressed with:
<source lang="python">
set cartoon_highlight_color, red
</source>

==Coloring all objects differently==
Is there a simple way to colour each object currently loaded, with a different colour?
There is a script [[Color_Objects |color_obj.py]] that does the job.

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

==List the color of atoms==
To retrieve the color for all residues in a selection, you can iterate over it from the PyMOL command line
<source lang="python">
iterate all, print color
</source>
In Python, it looks like this:
<source lang="python">
import pymol
pymol.color_list = []
cmd.iterate('all', 'pymol.color_list.append(color)')
print pymol.color_list
</source>

[[Category:Publication_Quality|Advanced Coloring]]
[[Category:Coloring|Advanced Coloring]]

PyMOL Wiki - User contributions [en]

Create

Advanced Coloring