PyMOL Wiki - User contributions [en]

Transparency

2006-06-27T19:54:59Z

Vossman: new page, needs help

'''Transparency''' is used to adjust the transparency of surfaces. To use try:

set transparency, 0.5

or

set transparency=0.5, selection

Where 1.0 will be an invisible and 0.0 a completely solid surface.

Mutagenesis

2006-05-11T20:40:48Z

Vossman: linearized for clarity

= Mutagenesis =
PyMol has a '''Mutagenesis Wizard''' to make mutagenesis very easy for the end user.

To mutate a residue follow these easy steps:
<OL>
<LI>Load a PDB file 

[[Image:Mutag1.png|180px|none]]
<LI>Under the '''Wizard''' menu select '''Mutagenesis''' 

[[Image:Mutag2.png|180px|none]]
<LI>In the PyMol viewer window select a residue 

[[Image:Mutag3.png|180px|none]]
<LI>Select '''No Mutation''' and select resultant residue 

[[Image:Mutag4.png|180px|none]]
<LI>Select Apply
<LI>Select Done
</OL>

Stereo ray

2006-04-25T18:48:57Z

Vossman: +manual method

[[Image:Stereo_ex_l.png|Left Image|200px|thumb|left]]
[[Image:Stereo_ex_r.png|Right Image|200px|thumb|right]]
[[Image:Stereo_complete.png|Combined Images|center|thumb|250px]]
 
== Manually ==

To get a stereo diagram you need to images. The left image is rotated +3 degrees and the right image is rotated -3 degrees.

To obtain the left image, type:
ray angle=+3
png left-image.png
Likewise, to obtasin the right image, type:
ray angle=-3
png right-image.png

You still use any other [[ray]] based modifications, such as:
ray 1600,1200,angle=+3
png big-left-image.png

== Script ==

A user on the PyMol list wrote a very nice little stereo ray tracing script. Just copy this to a text file. Then, in PyMol run
run dirName/scriptName.pym
where '''dirName''' is where you put it, and '''scriptName''' is what you named the file then run one something like the example lines given:
<source lang="python">
EXAMPLE
stereo_ray output, 1000, 600
stereo_ray secondImage.png
</source>
This will create to images, one with an L and one with an R suffix. Just paste the two images next to each other (in some image editing program) and you're done.

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

def stereo_ray(output='', width='', height=''):
'''
DESCRIPTION
"stereo_ray" ray-traces the current scene twice (separated by
a six-degree rotation around the y axis)
and saves a pair of images that can be combined in any image
manipulation software to form a stereoimage.
The first argument, the output file name, is mandatory.
The second and third arguments, the size of the image, are not.
If the width is given, the height will be calculated.

USAGE
stereo_ray filename [, width [, height]]

EXAMPLE
stereo_ray output, 1000, 600
stereo_ray secondImage.png
'''

if output == '':
print 'no output filename defined\n'
print 'try: \'stereo_ray filename\''
return -1
# abort if no output file name given

if width == '':
width,height = cmd.get_session()['main'][0:2]
# get dimensions from viewer if not given

elif height == '':
oldWidth,oldHeight = cmd.get_session()['main'][0:2]
height = int(width)*oldHeight/oldWidth
# calculate height from proportions of viewer if
# only width is given

cmd.ray(width, height, angle=-3)
cmd.png(output+"_r")
cmd.ray(width, height, angle=3)
cmd.png(output+"_l")

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

[[Category:Script_Library|Stereo Ray]]

Util.mroll

2006-03-20T22:28:46Z

Vossman: + See Alse

===DESCRIPTION===
'''util.mroll''' issues mdo commands to create full rotation

===USAGE===
util.mroll(start, finish, loop-flag)

=== EXAMPLE ===

In this next example, the protein is rotated through a full 360 sweep about the Y-axis over 120 frames

load test/dat/pept.pdb # load a structure
mset 1 x120 # define the movie
util.mroll(1,120,1) # issues [[mdo]] commands to create full rotation over 120 frames
mpng # outputs png files of rotation

=== SEE ALSO ===
* PyMol User Manual [http://pymol.sourceforge.net/newman/user/S0300movies.html Movie Page]

Util.mroll

2006-03-20T22:27:37Z

Vossman: /* EXAMPLE */

Util.mroll

2006-03-20T22:25:23Z

Vossman:

Spheres

2005-11-13T21:09:45Z

Vossman: Tip for changing sphere sizes

[[Image:Spheres_ex.png|thumb|Normal Sphere Representation Example|center]]

==Representation==
To enable the '''spheres''' representation do the following for any selection SEL,
show spheres, SEL

==Adjusting Sphere Size==

<source lang="python">
alter selection, vdw=number
</source>

===Examples===
Shrink the size of all Iron atoms:
<source lang="python">
alter elem fe, vdw=1.0
rebuild
</source>

Dramatically enlarge all spheres in an object
<source lang="python">
alter object, vdw=4.0
rebuild
</source>

==OpenGL Shaders & Spheres==
Newer OpenGL supported cards (like the NVidia 5950 Ultra, or the 6800 GT Ultra) support '''Shaders'''. Shaders are best used for massive numbers of molecules that are to be represented as spheres. Typical ranges will now include 500 000 to 3 000 000 atoms! Take a look, the following example is of a viral nucleocapsid: 261 240 atoms! Performance and visual quality -- without rendering -- are far improved.

===Comparing Shaders and No-Shaders===
[[Image:No_shader.jpg|thumb|Normal spheres: no shaders|center]]
[[Image:Shader.jpg|thumb|(sphere_mode=5) Shader Spheres|center]]

To turn on Sphere Shaders use
set sphere_mode, 5
as spheres, SEL
where '''SEL''' is the name of your selection. Getting normal sphere mode back is easy:
set sphere_mode, 4
as spheres, SEL

===Enabling Shaders===
If the above doesn't work, then you may need to rebuild PyMol so that it builds the shaders source code. To do this, you simply need to edit the '''setup.py''' file before you build PyMol.

Find the appropriate line in your '''setup.py''' file depending on your system. The relevant lines are, first for Windows,
<source lang="python">
if sys.platform=='win32':
</source>
and for Windows using Cygwin
<source lang="python">
elif sys.platform=='cygwin':
</source>
and finally for *nix or other systems as the following
<source lang="python">
else:
</source>
Under this code, find the
<source lang="python">
def_macros=[("_PYMOL_MODULE",None),
("_PYMOL_INLINE",None),
# ("_PYMOL_NUMPY",None),
("_HAVE_LIBPNG",None)]
</source>
and make it
<source lang="python">
def_macros=[("_PYMOL_MODULE",None),
("_PYMOL_INLINE",None),
# ("_PYMOL_NUMPY",None),
("_HAVE_LIBPNG",None),
("_PYMOL_OPENGL_SHADERS",None)]
</source>
I just added the
<source lang="python">
("_PYMOL_OPENGL_SHADERS",None)]
</source>
line.

See the [[:Category:Installation|Installation Page]] to find out how to build PyMol.

[[Category:Representations|Spheres]]

Color

2005-11-13T20:55:22Z

Vossman: adding technique to use RGB

===DESCRIPTION===
"color" changes the color of an object or an atom selection.

===USAGE===
color color-name
color color-name, object-name
color color-name, (selection)

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

==Using RGB for Color==
If you prefer RGB to color any object
<source lang="python">
set_color newcolor, [r,g,b]
color newcolor
</source>

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

RGB Example:
<source lang="python">
set_color khaki, [195,176,145]
color khaki
</source>

[[Category:Objects_and_Selections]]
[[Category:Commands|color]]

Cartoon

2005-10-24T14:20:02Z

Vossman: /* Adjusting width of cartoon */ info for loops; had to google it

==Cartoon Command==
===DESCRIPTION===
"cartoon" changes the default cartoon for a set of atoms.

===USAGE===
cartoon type, (selection)

type = skip | automatic | loop | rectangle | oval | tube | arrow | dumbbell

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

===EXAMPLES===
cartoon rectangle,(chain A)
cartoon skip,(resi 145:156)

===NOTES===
the "automatic" mode utilizes ribbons according to the
information in the PDB HELIX and SHEET records.

[[Category:Commands|cartoon]]

==Adjusting width of cartoon==

Try varying the following.

For β-strands:
<source lang="python">
cartoon_rect_length
cartoon_rect_width
</source>

For α-helices:
<source lang="python">
cartoon_oval_length
cartoon_oval_width
</source>

For loops:
<source lang="python">
cartoon_loop_radius
</source>

For "fancy" α-helices:
<source lang="python">
cartoon_dumbell_length
cartoon_dumbell_width
cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon)
</source>

In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.

[[Image:Cartoon_ex.png|thumb|center|Cartoon Representation Example|300px]]

===Forcing Exact Boundaries in Coloring Secondary Structures===
To force PyMol to respect secondary structural elements color-wise (PyMol smooths out colors near color chagnes for a prettier image) use the following
PyMol command:
<code>
set cartoon_discrete_colors, on
</code>

[[Image:Cartoon_discrete_color0.png|Discrete Coloring Off|center|thumb]] [[Image:Cartoon_discrete_color1.png|Discrete Coloring On|center|thumb]]

== Sausage Representation ==
The familiar sausage representation in PyMol is called, "putty". To enable the putty/sausage view simply do,
show cartoon
cartoon putty
unset cartoon_smooth_loops
unset cartoon_flat_sheets

As of v 0.98 or so, there's a Putty option. Use this.

[[Image:B_factor_putty.png|thumb|Example of B-factor Putty|center|250px]]

==Black and White Representation==
For those who want a nifty black and white representation of their protein try the following:
# Ray trace your protein of choice in a cartoon representation use a BLACK background
# Save the image
# Load the image in GIMP. [[Image:Bw1.jpeg|thumb|Black BG Ribbon|center|350px]]
# Desaturate or Grayscale the image. [[Image:Bw2.jpeg|thumb|Grayscale|center|350px]]
# Run the filter: Filter->Edge-Detect->Edge. [[Image:Bw3.jpeg|thumb|Edge Detect|center|350px]]
# Select: Layers->Color->Invert. [[Image:Bw4.jpeg|thumb|Invert Color|center|350px]]
# Different methods of edge detection will give you different results. In the last example, I used Laplace Edge-Detect, then painted an all white layer beneath the current layer to achieve the results. [[Image:Bw5.jpeg|thumb|Other Styles|center|350px|Comments]]

I'm sure there are other ways to do this. If you want to include it in a publication make sure you ray traced it large enough. For that, see [[:Category:Advanced_Issues_Image_Manipulation_Publication_Quatlity_Images|Creating Publication Quality Images]].

==CA (Alpha Carbon) Trace==
If you have a structure with just a alpha carbon trace, you can get a cartoon by
<source lang="python">
set cartoon_trace,1
show cartoon
</source>
If your structure is more than just the CA backbone, the cartoon representation will look incorrect, so use it just with CA trace.

==Various Transparency Levels==
[[Image:Cartoon_multi_transp.png|thumb|center|Example of Cartoon Multi-level Transparency. The near cartoon has transparency setting '''0.2''', the segment in the BG '''0.5'''.]]
One can make different cartoon selections have different transparency values, in PyMol. The trick here is to use "create" instead of "select". Create makes new objects that can have independent settings.

<source lang="python">
load mol_obj.pdb

# transfer a piece of the molecule into a new object

create new_obj, chain A
remove mol_obj in new_obj

# adjust trasparency for the new object

set cartoon_transparency, 0.5, new_obj
</source>

== Nucleic Acid Representation ==
[[Image:Nucleic1.png|thumb|center|Showing Nucleic Acids]]
To show nucleic acids in a nicer format do:
<source lang="python">
set cartoon_ring_mode,1
show cartoon
</source>

== See Also ==
[[Displaying_Biochemical_Properties]]

[[Category:Representations|Cartoon]]