PyMOL Wiki - User contributions [en]

Ray

2010-08-03T19:36:21Z

Vinnyrose: Describing the behavior of width and height.

'''ray''' creates a ray-traced image of the current frame.
[[Image:Gslike.png|right|350px|thumb|Varying settings to play with rendering options]]

=Details=
This command is used to make high-resolution photos fit for publication and formal movies. Please note, the '''ray''' command can take some time (up to several minutes, depending on image complexity and size).

For those who are making movies with PyMOL, '''Ray''' is one of the most commonly used last steps before stitching the frames together to compile the movie. '''Ray''' has many powerful features such as setting the size of the image -- and it still works even if the [[Viewport]] or screen is smaller than the requested output file dimensions.

[[Image:No_ray_trace.png|Image, not ray traced.|thumb|200px]] [[Image:ray_traced.png|Image, ray traced.|thumb|200px]]

==Usage==
ray [width,height [,renderer [,angle [,shift ]]]
'''angle''' and '''shift''' can be used to generate matched stereo pairs

'''width''' and '''height''' can be set to any non-negative integer. If both are set to zero than the current window size is used and is equivalent to just using '''ray''' with no arguments. If one is set to zero (or missing) while the other is a positive integer, then the argument set to zero (or missing) will be scaled to preserve the current aspect ratio.

==PyMol API==
<source lang="python">cmd.ray(int width,int height,int renderer=-1,float shift=0)</source>

==Settings==
===Modes===
Setting the '''[[Ray_trace_mode]]''' variable in PyMOL changes the way PyMOL's internal renderer represents proteins in the final output. New modes were recently added to give the user more options of molecular representation. New modes are: normal rendering, but with a black outline (nice for presentations); black and white only; quantized color with black outline (also, very nice for presentations; more of a ''cartoony'' appearance).

'''Note:''' Mode 3, the quantized color one, sort of '''burns''' the background if you're using this setting. This will make a pure white background somewhat "offwhite"; thus, a poster would look poor because you could see the border for the image. If you'll be using this mode, try the [[ray_opaque_background]] setting.

<source lang="python">
# normal color
set ray_trace_mode, 0

# normal color + black outline
set ray_trace_mode, 1

# black outline only
set ray_trace_mode, 2

# quantized color + black outline
set ray_trace_mode, 3

set ray_trace_mode, 1 # (or 2 or 3; best with "bg_color white;set antialias,2")
# These two new modes -- 2 and 3 -- are cool cartoon looking modes.
</source>

Here are the example images for the new modes
<gallery>
Image:Ray_mode_1_ex.png|set ray_trace_mode,1
Image:Ray_mode_2_ex.png|set ray_trace_mode,2
Image:Ray_mode_3_ex.png|set ray_trace_mode,3
</gallery>

===Perspective===
====Perspective Example Images====
<gallery>
Image:No_persp.png|Example with Perspective Turned Off
Image:Persp1.png|Example with Perspective Turned On
Image:Persp2.png|Example with Perspective Turned On and Field of View Set High (70).
</gallery>

=====Notes=====
PyMol 0.97 and prior used '''orthoscopic''' rendering -- that is, no perspective. Upon the arrival of 0.98 and later, we get perspective based rendering at a cost of a 4x decrease in render speed. If you want perspective
set orthoscopic, off
Otherwise
set orthoscopic, on
To magnify the effect of perspective on the scene,
set field_of_view, X
where 50<X<70. Default is 20. 50-70 gives a very strong perspective effect. Nb. the field of view is in Y, not X as one would expect.

===Renderer===
'''renderer = -1''' is default (use value in ray_default_renderer)

'''renderer = 0''' uses PyMOL's internal renderer

'''renderer = 1''' uses PovRay's renderer. This is Unix-only and you must have "x-povray" in your path. It utilizes two temporary files: "tmp_pymol.pov" and "tmp_pymol.png".

==Performance==
*The ray performance depends on distance between camera and molecule.
If the distance is big rendering takes much time. If the distance is too small distant parts of molecule dissolve.
<gallery>
Image:Close_ray.png|Too close to molecule
Image:Middle_ray.png|Normal distance
</gallery>
* Tip: If you have a rather complicated scene that is zoomed into only a part of the molecule, you can speed up the ray tracing by hiding everything else outside of a certain range of the zoomed-on point. For example, if I have a large molecule and I'm looking only at the 30-atom ligand bound to it, then I can do something like the following:
<source lang="python">
# setup your complex scene
...

# zoom on the hetero atom (ligand and not water) within 5 Angstroms
select hh, het and not resn HOH
zoom hh, 5

# turn on depth cueing
set depth_cue, 1

# now, select stuff to hide; we select everything that is
# farther than 8 Ang from our main selection
select th, (all) and not ( (all) within 8 of hh) )

hide everything, th

# any additional commands you want
...

ray
</source>
As an example of the efficacy of this method, I ray traced a rather complex scene with all the atoms visible here's the output of ray:
<source lang="bash">
PyMOL>ray
Ray: render time: 24.50 sec. = 146.9 frames/hour (941.88 sec. accum.).
</source>
and here is the result when I soft-clipped everything else using the above method:
<source lang="bash">
PyMOL>ray
Ray: render time: 47.93 sec. = 75.1 frames/hour (989.80 sec. accum.).
</source>
The two images in the following gallery show the results of the rendering.
<gallery>
Image:Ray_method_off.png|normal ray tracing. This took twice as long to make as the image to the right. Same size, and DPI.
Image:Ray_method_on.png|manually hiding things you won't see anyway. This took 1/2 the time to render as compared to the same sized & DPId image at left.
</gallery>

===Memory===
If memory is an issue for you in PyMOL, try executing your rendering from a script rather than a PyMOL session file. An unfortunate unavoidable consequence of the fact that we use Python's portable, platform-independent "pickle" machinery for PyMOL session files. Packing or unpacking a Session or Scene file thus requires that there be two simultanous copies of the information to reside in RAM simultaneously: one native and a second in Python itself.

So when memory is a limiting factor, scripts are recommended over sessions.

==Examples==
===Simple===
<source lang="python">
# ray trace the current scene using the default size of the viewport
ray
</source>

===Specify Image Size===
<source lang="python">
# ray trace the current scene, but scaled to 1024x768 pixels
ray 1024,768
</source>

===Specify Renderer===
<source lang="python">
# ray trace with an external renderer.
ray renderer=0
</source>

===High Quality B&W Rendering===
[[Image:1l9l.png|thumb|center|Black and White (ray_trace_mode,2); click to see full image]]
<source lang="python">
# Black and White Script
load /tmp/3fib.pdb;
show cartoon;
set ray_trace_mode, 2; # black and white cartoon
bg_color white;
set antialias, 2;
ray 600,600
png /tmp/1l9l.png
</source>

===High Quality Color===
[[Image:1l9l_2.png|thumb|center|Color mode (ray_trace_mode,3); click to see full image]]
<source lang="python">
# Color Script
load /tmp/thy_model/1l9l.pdb;
hide lines;
show cartoon;
set ray_trace_mode, 3; # color
bg_color white;
set antialias, 2;
remove resn HOH
remove resn HET
ray 600,600
png /tmp/1l9l.png
</source>

===Ray Tracing Stereo Images===
:''See [[Stereo_Ray]]''

==See also==
# "help faster" for optimization tips with the builtin renderer. "help povray" for how to use PovRay instead of PyMOL's built-in ray-tracing engine. For high-quality photos, please also see the [[Antialias]] command. [[Ray shadows]] for controlling shadows.
# See also [[Ray Tracing]].
# [http://www.gimp.org/tutorials/Color2BW Desaturation Tutorial] -- A good resource for making nice B&W images from color images (desaturation).

==User comments==
;How do I ray trace a publication-ready (~300dpi) image using PyMol?
:This answer is in the [[:Category:Advanced_Issues|Advanced Issues]] (Image Manipulation Section).

[[Category:Commands|Ray]]
[[Category:Publication_Quality|Ray]]
[[Category:Performance|Ray]]
[[Category:Movies|Ray]]

Ray

2010-08-03T19:34:18Z

Vinnyrose:

'''ray''' creates a ray-traced image of the current frame.
[[Image:Gslike.png|right|350px|thumb|Varying settings to play with rendering options]]

=Details=
This command is used to make high-resolution photos fit for publication and formal movies. Please note, the '''ray''' command can take some time (up to several minutes, depending on image complexity and size).

For those who are making movies with PyMOL, '''Ray''' is one of the most commonly used last steps before stitching the frames together to compile the movie. '''Ray''' has many powerful features such as setting the size of the image -- and it still works even if the [[Viewport]] or screen is smaller than the requested output file dimensions.

[[Image:No_ray_trace.png|Image, not ray traced.|thumb|200px]] [[Image:ray_traced.png|Image, ray traced.|thumb|200px]]

==Usage==
ray [width,height [,renderer [,angle [,shift ]]]
'''angle''' and '''shift''' can be used to generate matched stereo pairs

'''width''' and '''height''' can be set to any non-negative numbers. If both are set to zero than the current window size is used and is equivalent to just using "ray" with no arguments. If one is set to zero (or missing) while the other is non-zero and positive, then the argument set to zero (or missing) will be scaled to preserve the current aspect ratio.

==PyMol API==
<source lang="python">cmd.ray(int width,int height,int renderer=-1,float shift=0)</source>

==Settings==
===Modes===
Setting the '''[[Ray_trace_mode]]''' variable in PyMOL changes the way PyMOL's internal renderer represents proteins in the final output. New modes were recently added to give the user more options of molecular representation. New modes are: normal rendering, but with a black outline (nice for presentations); black and white only; quantized color with black outline (also, very nice for presentations; more of a ''cartoony'' appearance).

'''Note:''' Mode 3, the quantized color one, sort of '''burns''' the background if you're using this setting. This will make a pure white background somewhat "offwhite"; thus, a poster would look poor because you could see the border for the image. If you'll be using this mode, try the [[ray_opaque_background]] setting.

<source lang="python">
# normal color
set ray_trace_mode, 0

# normal color + black outline
set ray_trace_mode, 1

# black outline only
set ray_trace_mode, 2

# quantized color + black outline
set ray_trace_mode, 3

set ray_trace_mode, 1 # (or 2 or 3; best with "bg_color white;set antialias,2")
# These two new modes -- 2 and 3 -- are cool cartoon looking modes.
</source>

Here are the example images for the new modes
<gallery>
Image:Ray_mode_1_ex.png|set ray_trace_mode,1
Image:Ray_mode_2_ex.png|set ray_trace_mode,2
Image:Ray_mode_3_ex.png|set ray_trace_mode,3
</gallery>

===Perspective===
====Perspective Example Images====
<gallery>
Image:No_persp.png|Example with Perspective Turned Off
Image:Persp1.png|Example with Perspective Turned On
Image:Persp2.png|Example with Perspective Turned On and Field of View Set High (70).
</gallery>

=====Notes=====
PyMol 0.97 and prior used '''orthoscopic''' rendering -- that is, no perspective. Upon the arrival of 0.98 and later, we get perspective based rendering at a cost of a 4x decrease in render speed. If you want perspective
set orthoscopic, off
Otherwise
set orthoscopic, on
To magnify the effect of perspective on the scene,
set field_of_view, X
where 50<X<70. Default is 20. 50-70 gives a very strong perspective effect. Nb. the field of view is in Y, not X as one would expect.

===Renderer===
'''renderer = -1''' is default (use value in ray_default_renderer)

'''renderer = 0''' uses PyMOL's internal renderer

'''renderer = 1''' uses PovRay's renderer. This is Unix-only and you must have "x-povray" in your path. It utilizes two temporary files: "tmp_pymol.pov" and "tmp_pymol.png".

==Performance==
*The ray performance depends on distance between camera and molecule.
If the distance is big rendering takes much time. If the distance is too small distant parts of molecule dissolve.
<gallery>
Image:Close_ray.png|Too close to molecule
Image:Middle_ray.png|Normal distance
</gallery>
* Tip: If you have a rather complicated scene that is zoomed into only a part of the molecule, you can speed up the ray tracing by hiding everything else outside of a certain range of the zoomed-on point. For example, if I have a large molecule and I'm looking only at the 30-atom ligand bound to it, then I can do something like the following:
<source lang="python">
# setup your complex scene
...

# zoom on the hetero atom (ligand and not water) within 5 Angstroms
select hh, het and not resn HOH
zoom hh, 5

# turn on depth cueing
set depth_cue, 1

# now, select stuff to hide; we select everything that is
# farther than 8 Ang from our main selection
select th, (all) and not ( (all) within 8 of hh) )

hide everything, th

# any additional commands you want
...

ray
</source>
As an example of the efficacy of this method, I ray traced a rather complex scene with all the atoms visible here's the output of ray:
<source lang="bash">
PyMOL>ray
Ray: render time: 24.50 sec. = 146.9 frames/hour (941.88 sec. accum.).
</source>
and here is the result when I soft-clipped everything else using the above method:
<source lang="bash">
PyMOL>ray
Ray: render time: 47.93 sec. = 75.1 frames/hour (989.80 sec. accum.).
</source>
The two images in the following gallery show the results of the rendering.
<gallery>
Image:Ray_method_off.png|normal ray tracing. This took twice as long to make as the image to the right. Same size, and DPI.
Image:Ray_method_on.png|manually hiding things you won't see anyway. This took 1/2 the time to render as compared to the same sized & DPId image at left.
</gallery>

===Memory===
If memory is an issue for you in PyMOL, try executing your rendering from a script rather than a PyMOL session file. An unfortunate unavoidable consequence of the fact that we use Python's portable, platform-independent "pickle" machinery for PyMOL session files. Packing or unpacking a Session or Scene file thus requires that there be two simultanous copies of the information to reside in RAM simultaneously: one native and a second in Python itself.

So when memory is a limiting factor, scripts are recommended over sessions.

==Examples==
===Simple===
<source lang="python">
# ray trace the current scene using the default size of the viewport
ray
</source>

===Specify Image Size===
<source lang="python">
# ray trace the current scene, but scaled to 1024x768 pixels
ray 1024,768
</source>

===Specify Renderer===
<source lang="python">
# ray trace with an external renderer.
ray renderer=0
</source>

===High Quality B&W Rendering===
[[Image:1l9l.png|thumb|center|Black and White (ray_trace_mode,2); click to see full image]]
<source lang="python">
# Black and White Script
load /tmp/3fib.pdb;
show cartoon;
set ray_trace_mode, 2; # black and white cartoon
bg_color white;
set antialias, 2;
ray 600,600
png /tmp/1l9l.png
</source>

===High Quality Color===
[[Image:1l9l_2.png|thumb|center|Color mode (ray_trace_mode,3); click to see full image]]
<source lang="python">
# Color Script
load /tmp/thy_model/1l9l.pdb;
hide lines;
show cartoon;
set ray_trace_mode, 3; # color
bg_color white;
set antialias, 2;
remove resn HOH
remove resn HET
ray 600,600
png /tmp/1l9l.png
</source>

===Ray Tracing Stereo Images===
:''See [[Stereo_Ray]]''

==See also==
# "help faster" for optimization tips with the builtin renderer. "help povray" for how to use PovRay instead of PyMOL's built-in ray-tracing engine. For high-quality photos, please also see the [[Antialias]] command. [[Ray shadows]] for controlling shadows.
# See also [[Ray Tracing]].
# [http://www.gimp.org/tutorials/Color2BW Desaturation Tutorial] -- A good resource for making nice B&W images from color images (desaturation).

==User comments==
;How do I ray trace a publication-ready (~300dpi) image using PyMol?
:This answer is in the [[:Category:Advanced_Issues|Advanced Issues]] (Image Manipulation Section).

[[Category:Commands|Ray]]
[[Category:Publication_Quality|Ray]]
[[Category:Performance|Ray]]
[[Category:Movies|Ray]]

Talk:ProMOL

2009-07-30T17:15:00Z

Vinnyrose: Blanked the page

Category:Colour Module

2009-06-22T21:43:44Z

Vinnyrose:

#REDIRECT[[:Category:Color_Module]].

[[Category:Commands]]

Category:Colour Module

2009-06-20T15:22:24Z

Vinnyrose: Redirected page to Category:Color Module

#REDIRECT[[Category:Color_Module]].

[[Category:Commands]]

Category:Colour Module

2009-06-20T15:21:30Z

Vinnyrose:

#REDIRECT [Category:Color_Module].

[[Category:Commands]]

Category:Colour Module

2009-06-20T15:19:51Z

Vinnyrose: Redirected page to Category:Color Module

#REDIRECT [[Category:Color_Module]].

[[Category:Commands]]

Category:Colour Module

2009-06-20T15:19:10Z

Vinnyrose: Redirected page to Color Module

#REDIRECT [[Color Module]].

[[Category:Commands]]

Category:Language Module

2009-06-20T15:17:06Z

Vinnyrose: Created page with 'This is a list of all commands in the Language Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Language Module for PyMol's interface.

[[Category:Commands]]

Category:Scripts Module

2009-06-20T15:16:25Z

Vinnyrose: Created page with 'This is a list of all commands in the Scripts Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Scripts Module for PyMol's interface.

[[Category:Commands]]

Category:Symmetry Module

2009-06-20T15:16:01Z

Vinnyrose: Created page with 'This is a list of all commands in the Symmetry Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Symmetry Module for PyMol's interface.

[[Category:Commands]]

Category:Stereo Module

2009-06-20T15:15:34Z

Vinnyrose: Created page with 'This is a list of all commands in the Stereo Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Stereo Module for PyMol's interface.

[[Category:Commands]]

Category:Distances Module

2009-06-20T15:15:12Z

Vinnyrose: Created page with 'This is a list of all commands in the Distances Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Distances Module for PyMol's interface.

[[Category:Commands]]

Category:Help Module

2009-06-20T15:14:44Z

Vinnyrose: Created page with 'This is a list of all commands in the Help Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Help Module for PyMol's interface.

[[Category:Commands]]

Category:Color Module

2009-06-20T15:14:25Z

Vinnyrose: Created page with 'This is a list of all commands in the Color Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Color Module for PyMol's interface.

[[Category:Commands]]

Category:Fitting Module

2009-06-20T15:13:49Z

Vinnyrose: Created page with 'This is a list of all commands in the Fitting Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Fitting Module for PyMol's interface.

[[Category:Commands]]

Category:Atoms Module

2009-06-20T15:13:22Z

Vinnyrose: Created page with 'This is a list of all commands in the Atoms Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Atoms Module for PyMol's interface.

[[Category:Commands]]

Category:Settings Module

2009-06-20T15:13:02Z

Vinnyrose: Created page with 'This is a list of all commands in the Settings Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Settings Module for PyMol's interface.

[[Category:Commands]]

Category:Selections Module

2009-06-20T15:12:06Z

Vinnyrose: Created page with 'This is a list of all commands in the Selections Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Selections Module for PyMol's interface.

[[Category:Commands]]

Category:Display Module

2009-06-20T15:11:35Z

Vinnyrose: Created page with 'This is a list of all commands in the Display Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Display Module for PyMol's interface.

[[Category:Commands]]

Category:Maps Module

2009-06-20T15:11:16Z

Vinnyrose: Created page with 'This is a list of all commands in the Maps Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Maps Module for PyMol's interface.

[[Category:Commands]]

Category:Ray Tracing Module

2009-06-20T15:10:52Z

Vinnyrose: Created page with 'This is a list of all commands in the Ray Tracing Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Ray Tracing Module for PyMol's interface.

[[Category:Commands]]

Category:Imaging Module

2009-06-20T15:10:14Z

Vinnyrose: Created page with 'This is a list of all commands in the Imaging Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Imaging Module for PyMol's interface.

[[Category:Commands]]

Category:Movies Module

2009-06-20T15:09:35Z

Vinnyrose: Created page with 'This is a list of all commands in the Movies Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Movies Module for PyMol's interface.

[[Category:Commands]]

Show as

2009-06-20T15:08:52Z

Vinnyrose:

== DESCRIPTION ==
(History: Python 2.6 came out with the keyword [[as]] which is also a PyMOL keyword. So, we had to change the PyMOL-named keyword to [[show_as]].)

[[show_as]] turns on and off atom and bond [[:Category:Representations|representations]], where the available representations are the usual:
*[[lines]]
*[[spheres]]
*[[mesh]]
*[[ribbon]]
*[[cartoon]]
*[[sticks]]
*[[dots]]
*[[surface]]
*[[labels]]
*[[extent]]
*[[nonbonded]]
*[[nb_spheres]]
*[[slice]]

== USAGE ==
<source lang="python">
show_as representation [, selection ]
</source>

== ARGUMENTS ==
*'''representation''' = lines, spheres, mesh, ribbon, cartoon, sticks, dots, surface, labels, extent, nonbonded, nb_spheres, slice, extent, slice, dashes, angles, dihedrals, cgo, cell, callback, everything
*'''selection''' = string {default: all}

== EXAMPLES ==
<source lang="python">
# show the backbone as lines
show_as lines, name ca or name c or name n

# show everything as a ribbon
show_as ribbon
</source>
== PYMOL API ==
<source lang="python">
cmd.show_as(string representation, string selection)
</source>

== NOTES ==
*'''selection''' can be an object name
*'''as''' alone will turn on lines and nonbonded and hide everything else.

== SEE ALSO ==
[[show]], [[hide]], [[enable]], [[disable]], [[:Category:Representations|All PyMOL Representations]]

== References ==
* PyMOL Source code

[[Category:Commands|Show As]]
[[Category:View Module|Show As]]

Show

2009-06-20T15:07:52Z

Vinnyrose:

<gallery widths="125px" heights="125px" align="right">
Image:Ray2.png|Example of a shown surface.
Image:Ray_trace_gain2.png|Ball and sticks shown.
Image:Mesh_w05.png|A cartoon inside a mesh shown.
</gallery>

==DESCRIPTION==
'''Show''' displays atom and bond representations for certain selections. The '''Show''' command, is one of the most often used commands in PyMOL. For example, you can ''show'' certain atoms as ''[[Lines]]'' or ''[[Sticks]]'' or ''[[Cartoon]]s'' or any of the following representations:
*[[lines]]
*[[spheres]]
*[[mesh]]
*[[ribbon]]
*[[cartoon]]
*[[sticks]]
*[[dots]]
*[[surface]]
*[[Label|label]]
*[[extent]]
*[[nonbonded]]
*[[nb_spheres]]
*[[slice]]
*[[cell]]

==USAGE==
show
show reprentation [,object]
show reprentation [,(selection)]
show (selection)

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

==EXAMPLES==
====Example====
<source lang="python">
# show the backbone using lines.
show lines,(name ca or name c or name n)
</source>

====Example====
<source lang="python">
# show the ribbon representation for all objects
show ribbon
</source>

====Example====
<source lang="python">
# show all hetero atoms as spheres
show spheres, het
</source>

====Example====
<source lang="python">
# show only polar hydrogens
hide everything, ele h
show lines, ele h and neighbor (ele n+o)
</source>

==NOTES==
'''selection''' can be an object name.

'''show''' alone will turn on lines and nonbonded for all bonds.

'''show cell''' will show the triclinic unit cell, provided it's described in the PDB. For cell packing, you need a script. See [[:Category:Script_Library|The Script Library]] or [http://adelie.biochem.queensu.ca/~rlc/work/pymol/ Robert Campbell's Site]

==SEE ALSO==
[[Hide]], [[Enable]], [[Disable]], [[Lines]], [[Cartoon]], [[Spheres]], [[Mesh]], [[Ribbon]], [[Sticks]], [[Dots]], [[Surface]], [[Label]], [[Extent]], [[Slice]], [[Cell]], [[Select]], [[Show_as]]

[[Category:Commands|Show]]
[[Category:View Module|Show]]

Set View

2009-06-20T15:07:17Z

Vinnyrose:

===DESCRIPTION===
'''set_view''' sets viewing information for the current scene, including the rotation matrix, position, origin of rotation, clipping planes, and the orthoscopic flag.

This command is extremely useful for making movies. One may set up the scene to be rendered, then save the exact orientation, with respect to the camera, of the scene using, the [[Get_View]] command. The output from the [[Get_View]] command may then be used by the '''set_view''' command to restore the orientation of the scene.

===USAGE===
set_view (...) where ... is 18 floating point numbers

===PYMOL API===
<source lang="python">
cmd.set_view(string-or-sequence view)
</source>

===NOTES===
Contents of the view matrix
*0 - 8 = 3x3 rotation matrix which transforms model to camera space
*9 - 11 = camera position (in model space and relative to the origin of rotation)
*12 - 14 = origin of rotation (in model space)
*15 = front plane distance from the camera
*16 = rear plane distance from the camera
*17 = not implemented (the online help says that this should be the orthoscopic view flag, but PyMol as of v0.99 does not implement this)

===SEE ALSO===
[[Get View]]

[[Category:Commands|Set View]]
[[Category:View Module|Set View]]

Get View

2009-06-20T15:07:01Z

Vinnyrose:

===DESCRIPTION===
'''get_view''' returns and optionally prints out the current view information in a format which can be embedded into a command script and can be used in subsequent calls to '''set_view'''.

If a log file is currently open, get_view will not write the view matrix to the screen unless the "output" parameter is 2.

This command is very useful for saving the orientation of a scene for later. Authors of molecular movies may find this command very powerful.

===USAGE===
get_view

===PYMOL API===
<source lang="python">
cmd.get_view(output=1,quiet=1)

my_view= cmd.get_view()
</source>

output control:
*0 = output matrix to screen
*1 = don't output matrix to screen
*2 = force output to screen even if log file is open
*3 = return formatted string instead of a list

===API USAGE===
<source lang="python">
cmd.get_view(0) # zero option suppresses output (LEGACY approach)
cmd.get_view(quiet=1) # suppresses output using PyMOL's normal "quiet" parameter.
</source>

===NOTES===
Contents of the view matrix
*0 - 8 = 3x3 rotation matrix which transforms model to camera space
*9 - 11 = camera position (in model space and relative to the origin of rotation)
*12 - 14 = origin of rotation (in model space)
*15 = front plane distance from the camera
*16 = rear plane distance from the camera
*17 = orthoscopic flag

===SEE ALSO===
[[Set View]]

[[Category:Commands|Get View]]
[[Category:View Module|Get View]]

View

2009-06-20T15:06:48Z

Vinnyrose:

===DESCRIPTION===
'''view''' makes it possible to save and restore viewpoints on a given scene within a single session.

===USAGE===
<source lang="python">
view key[,action]
view *
</source>

key can be any string
action should be 'store' or 'recall' (default: 'recall')

===PYMOL API===
<source lang="python">
cmd.view(string key,string action)
</source>

===VIEWS===
Views F1 through F12 are automatically bound to function keys provided that "set_key" has not been used to redefine the behaviour of the respective key, and that a "scene" has not been defined for that key.

===EXAMPLES===
view 0,store
view 0

===SEE ALSO===
[[Scene]], [[Set View]], [[Get View]]

[[Category:Commands|View]]
[[Category:View Module|View]]

Origin

2009-06-20T15:06:10Z

Vinnyrose:

===DESCRIPTION===
'''origin''' sets the center of rotation about a selection. If an object name is specified, it can be used to set the center of rotation for the object's TTT matrix.

===USAGE===
<source lang="python">
origin selection [, object [,position, [, state]]]
origin (selection)
origin position=[1.0,2.0,3.0]
</source>

===PYMOL API===
<source lang="python">
cmd.origin( string object-or-selection )
</source>

===NOTES===
* state = 0 (default) use all coordinate states
* state = -1 use only coordinates for the current state
* state > 0 use coordinates for a specific state

===SEE ALSO===
[[Zoom]], [[Orient]], [[Reset]]

[[Category:Commands|Origin]]
[[Category:States|Origin]]
[[Category:View Module|Origin]]

Zoom

2009-06-20T15:05:43Z

Vinnyrose:

===DESCRIPTION===
'''zoom''' scales and translates the window and the origin to cover the atom selection.

===USAGE===
zoom [ selection [,buffer [, state [, complete ]]]]

===EXAMPLES===
<source lang="python">
# auto zoom depending on what's loaded in PyMOL
zoom

#
zoom complete=1

# zoom on just chain A
zoom (chain A)

# zoom on residue 142
zoom 142/

# zoom consistenly 20 Ang from each object at the center
center prot1
zoom center, 20

# prot1 and prot2 will have the same exact zoom factor
center prot2
zoom center, 20
</source>

===PYMOL API===
<source lang="python">
cmd.zoom( string selection, float buffer=0.0,
int state=0, int complete=0 )
</source>

===NOTES===
state = 0 (default) use all coordinate states
state = -1 use only coordinates for the current state
state > 0 use coordinates for a specific state

complete = 0 or 1:

Normally the zoom command tries to guess an optimal zoom level for visualization, balancing closeness against occasional clipping of atoms out of the field of view. You can change this behavior by setting the complete option to 1, which will guarantee that the atom positions for the entire selection will fit in the field of an orthoscopic view. To absolutely prevent clipping, you may also need to add a buffer (typically 2 A) to account for the perspective transformation and for graphical representations which extend beyond the atom coordinates.

===SEE ALSO===
*[[Origin]]
*[[Orient]]
*[[Center]]

[[Category:Commands|Zoom]]
[[Category:States|Zoom]]
[[Category:View Module|Zoom]]

Rebuild

2009-06-20T15:05:29Z

Vinnyrose:

===DESCRIPTION===
'''rebuild''' forces PyMOL to recreate geometric objects in case any of them have gone out of sync.

===USAGE===
rebuild [selection [, representation ]]

===PYMOL API===
<source lang="python">
cmd.rebuild(string selection = 'all', string representation = 'everything')
</source>

===SEE ALSO===
[[refresh]]

[[Category:Commands|Rebuild]]
[[Category:View Module|Rebuild]]

Refresh

2009-06-20T15:05:13Z

Vinnyrose:

===DESCRIPTION===
'''refresh''' causes the scene to be refresh as soon as it is safe to do so.

===USAGE===
refresh

===PYMOL API===
<source lang="python">
cmd.refresh()
</source>

===SEE ALSO===
[[rebuild ]]

[[Category:Commands|Refresh]]
[[Category:View Module|Refresh]]

Reset

2009-06-20T15:05:03Z

Vinnyrose:

===DESCRIPTION===
'''reset''' restores the rotation matrix to identity, sets the origin to the center of mass (approx.) and zooms the window and clipping planes to cover all objects.

===USAGE===
reset

===PYMOL API===
<source lang="python">
cmd.reset()
</source>

==SEE ALSO==
[[Cmd clip]] [[Cmd zoom]]

[[Category:Commands|Reset]]
[[Category:View Module|Reset]]

Disable

2009-06-20T15:04:54Z

Vinnyrose:

===DESCRIPTION===
'''disable''' disables display of an object and all currently visible representations.

===USAGE===
disable name
disable all

'''name''' is the name of an object or a named selection

===PYMOL API===
<source lang="python">
cmd.disable( string name )
</source>

===EXAMPLE===
disable my_object

===SEE ALSO===
[[Show]], [[Hide]], [[Enable]]

[[Category:Commands|Disable]]
[[Category:View Module|Disable]]

Enable

2009-06-20T15:04:42Z

Vinnyrose:

===DESCRIPTION===
'''enable''' enable display of an object and all currently visible representations.

===USAGE===
enable name
enable all
name = object or selection name

===PYMOL API===
<source lang="python">
cmd.enable( string object-name )
</source>

===EXAMPLE===
enable my_object

===SEE ALSO===
[[Show]], [[Hide]], [[Disable]]

[[Category:Commands|Enable]]
[[Category:View Module|Enable]]

Hide

2009-06-20T15:04:32Z

Vinnyrose:

===DESCRIPTION===
'''hide''' conceals atom and bond representations for a certain selection or other graphical objects like distances.

<gallery>
Image:Show1.png|Some normal scene, notice the waters shown as spheres
Image:Show2.png|''hide spheres'' issues and the spheres are now hidden.
</gallery>

The available representations are:
*lines
*spheres
*mesh
*ribbon
*cartoon
*sticks
*dots
*surface
*labels
*nonbonded
*nb_spheres

===USAGE===
<source lang="python">
hide representation [,object]
hide representation [,(selection)]
hide (selection)
</source>

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

===EXAMPLES===
<source lang="python">
# hides all lines
hide lines,all

# hides all ribbons
hide ribbon

# hides all distances
hide dashes

# hides sticks in protA and all residues that aren't in the range of 40-65
hide sticks, protA and not i. 40-65
</source>

===SEE ALSO===
[[Show]], [[Enable]], [[Disable]]

[[Category:Commands|Hide]]
[[Category:View Module|Hide]]

Rock

2009-06-20T15:01:00Z

Vinnyrose:

===DESCRIPTION===
'''rock''' toggles Y axis rocking.

===USAGE===
rock

===PYMOL API===
<source lang="python">
cmd.rock()
</source>

[[Category:Commands|Rock]]
[[Category:View Module|Rock]]

Clip

2009-06-20T15:00:45Z

Vinnyrose:

===DESCRIPTION===
'''clip''' alters the near and far clipping planes

===USAGE===
clip {near|far|move|slab|atoms}, distance [,selection [,state ]]

===EXAMPLES===
clip near, -5 # moves near plane away from you by 5 A
clip far, 10 # moves far plane towards you by 10 A
clip move, -5 # moves the slab away from you by 5 A
clip slab, 20 # sets slab thickness to 20 A
clip slab, 10, resi 11 # clip 10 A slab about residue 11
clip atoms, 5, pept # clip atoms in "pept" with a 5 A buffer
# about their current camera positions
==PYMOL API==
<source lang="python">
cmd.clip( string mode, float distance, string selection = None)
</source>

==SEE ALSO==
*[[Zoom]]
*[[Reset]]

[[Category:Commands|Clip]]
[[Category:States|Clip]]
[[Category:View Module|Clip]]

Move

2009-06-20T15:00:33Z

Vinnyrose:

===DESCRIPTION===
'''move''' translates the camera about one of the three primary axes.

===USAGE===
move axis,distance

====EXAMPLES====
move x,3
move y,-1

===PYMOL API===
<source lang="python">
cmd.move( string axis, float distance )
</source>

===SEE ALSO===
[[Cmd turn]], [[Cmd rotate]], [[Cmd translate]], [[Cmd zoom]], [[Cmd center]], [[Cmd clip]], [[Translate]]

[[Category:Commands|Move]]
[[Category:View Module|Move]]

Turn

2009-06-20T15:00:24Z

Vinnyrose:

===DESCRIPTION===
'''turn''' rotates the camera about one of the three primary axes, centered at the origin. Also consider [[rotate]].

===USAGE===
turn axis, angle

===EXAMPLES===
turn x,90
turn y,45

===PYMOL API===
<source lang="python">
cmd.turn( string axis, float angle )
</source>

===SEE ALSO===
[[move]], [[rotate]], [[translate]], [[zoom]], [[center]], [[clip]]

[[Category:Commands|Turn]]
[[Category:View Module|Turn]]

Category:View Module

2009-06-20T14:58:04Z

Vinnyrose: Created page with 'This is a list of all commands in the View Module for PyMol's interface. Category:Commands'

This is a list of all commands in the View Module for PyMol's interface.

[[Category:Commands]]

Quit

2009-06-20T14:56:59Z

Vinnyrose:

===DESCRIPTION===
'''quit''' terminates the program.

===USAGE===
quit

===PYMOL API===
<source lang="python">
cmd.quit()
</source>

[[Category:Commands|Quit]]
[[Category:Input Output Module|Quit]]

Save

2009-06-20T14:56:40Z

Vinnyrose:

===DESCRIPTION===
'''save''' writes selected atoms to a file. The file format is
autodetected if the extesion is ".pdb", ".pse", ".mol", ".mmod", or
".pkl"

Note that if the file extension ends in ".pse" (PyMOL Session), the
complete PyMOL state is always saved to the file (the selection and
state parameters are thus ignored).

===USAGE===
<source lang="python">
save file [,(selection) [,state [,format]] ]
</source>
===PYMOL API===
<source lang="python">
cmd.save(file, selection, state, format)
</source>

===NOTES===
* When saving a session file, then "state" has no effect.
* When state = 0 (default), only the current state is written.
* When state = -1, then a multi-state output file is written (PDB only).

* In versions 1.XX, a multi-state output file is written when state = 0 (which is not default)
===SEE ALSO===
[[Load]], [[Get Model]]

[[Category:Commands|Save]]
[[Category:States|Save]]
[[Category:Input Output Module|Save]]

Delete

2009-06-20T14:56:08Z

Vinnyrose:

===DESCRIPTION===
'''delete''' removes an object or a selection.

===USAGE===
<source lang="python">
delete name
delete all # deletes all objects</source>

name = name of object or selection

===PYMOL API===
<source lang="python">
cmd.delete(string name = object-or-selection-name )
</source>

===SEE ALSO===
[[Remove|Remove]]

[[Category:Commands|Delete]]
[[Category:Input Output Module|Delete]]

Delete

2009-06-20T14:55:38Z

Vinnyrose:

===DESCRIPTION===
'''delete''' removes an object or a selection.

===USAGE===
<source lang="python">
delete name
delete all # deletes all objects</source>

name = name of object or selection

===PYMOL API===
<source lang="python">
cmd.delete(string name = object-or-selection-name )
</source>

===SEE ALSO===
[[Cmd Remove|Remove]]

[[Category:Commands|Delete]]
[[Category:Input Output Module|Delete]]

Load

2009-06-20T14:55:07Z

Vinnyrose:

===DESCRIPTION===
'''load''' reads several file formats. The file extension is used to determine the format. PDB files must end in ".pdb", MOL files must end in ".mol", Macromodel files must end in ".mmod", XPLOR maps must end in ".xplor", CCP4 maps must end in ".ccp4", Raster3D input (Molscript output) must end in ".r3d", PyMOL session files must end in ".pse", and pickled ChemPy models with a ".pkl" can also be directly read.

If an object is specified, then the file is loaded into that object. Otherwise, an object is created with the same name as the file prefix.

===USAGE===
<source lang="python">
load filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]]
</source>

===PYMOL API===
<source lang="python">
cmd.load( filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]] )
</source>

===NOTES===
*You can override the file extension by giving a format string:

'pdb' : PDB, 'mmod' : Macromodel, 'xyz' : Tinker, 'cc1' : ChemDraw3D
'mol' : MDL MOL-file, 'sdf' : MDL SD-file
'xplor' : X-PLOR/CNS map, 'ccp4' : CCP4 map,
'callback' : PyMOL Callback object (PyOpenGL)
'cgo' : compressed graphics object (list of floats)
'trj' : AMBER trajectory (use load_traj command for more control)
'top' : AMBER topology file 'rst' : AMBER restart file
'cex' : Metaphorics CEX format
'pse' : PyMOL Session file
'pqr' : PQR (a modified PDB file with charges and radii)
'mol2' : MOL2

* A new feature has been added to load. You can specify an URL to a PDB and PyMOL will download it. This is a very handy feature for loading experimental/theoretical data from servers across the web. Just copy the link they give you and do,
<source lang="python">
load http://www.theurl.com/path/toYourData
</source>
or you can open a remote file just from the command line
<source lang="bash">
# load a PDB file; I placed one example file on the PyMOL Wiki
pymol http://www.pymolwiki.org/1rsy.pdb

# PyMOL can also handle the gzipped files on the PDB. :-)
pymol ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/00/pdb100d.ent.gz
</source>

===User Comments/Examples===
*Load xyz.pdb using the PyMOL API:
<source lang="python">
cmd.load("xyz.pdb")
</source>

* Loading multiple PDBs into one object with many states:
<source lang="python">
load trj0001.pdb, mov
load trj0002.pdb, mov
load trj0003.pdb, mov
etc.
</source>
or, if you have too many states to do that by hand,
<source lang="python">
for idx in range(1,1001):cmd.load("trj%04d.pdb"%idx,"mov")
</source>
or, you can use "glob" from Python,
<source lang="python">
from glob import glob
lst = glob("trj*.pdb")
lst.sort()
for fil in lst: cmd.load(fil,"mov")
</source>

*Load a NAMD multi-PDB file. These are just concatenated PDB files.
<source lang="python">
load NAMDtrajFile.pdb, multiplex=0
</source>

* Hint: You can save some time & a lot of memory by loading the file and removing the atoms in a single-line compound statement (with a semicolon
after the load statement).
<source lang="python">
load 1E3M.pdb; remove not A-C+F//
</source>

===SEE ALSO===
[[Save]] [[Load Traj]]

[[Category:Commands|Load]]
[[Category:States|Load]]
[[Category:Input Output Module|Load]]

Category:Input Output Module

2009-06-20T14:53:19Z

Vinnyrose: Created page with 'This is a list of all commands in the Input/Output Module for PyMol's interface. Category:Commands'

This is a list of all commands in the Input/Output Module for PyMol's interface.

[[Category:Commands]]

Attach

2009-06-20T14:49:10Z

Vinnyrose:

==DESCRIPTION==
'''attach''' adds a single atom onto the picked atom.

==USAGE==
attach element, geometry, valence

==PYMOL API==
cmd.attach( element, geometry, valence )

==NOTES==
Immature functionality. See code for details.

[[Category:Commands|Attach]]
[[Category:Editing Module|Attach]]

Fuse

2009-06-20T14:48:57Z

Vinnyrose:

===DESCRIPTION===
'''fuse''' joins two objects into one by forming a bond. A copy of
the object containing the first atom is moved so as to form an
approximately resonable bond with the second, and is then merged
with the first object.

===USAGE===
fuse (selection1), (selection2)

===PYMOL API===
<source lang="python">
cmd.fuse( string selection1="(pk1)", string selection2="(pk2)" )
</source>

===NOTES===
Each selection must include a single atom in each object.
The atoms can both be hydrogens, in which case they are
eliminated, or they can both be non-hydrogens, in which
case a bond is formed between the two atoms.

===SEE ALSO===
[[Bond]], [[Unbond]], [[Attach]], [[Replace]], [[Fuse]], [[Remove_picked]]

[[Category:Commands|Fuse]]
[[Category:Editing Module|Fuse]]