[PyMOL] POVRAY Usage

[Sean Law]

Hi All,

While ray tracing a scene with 10 x-large proteins in grid mode at 3600, 3600 (width, height) I ran out of RAM (2 GB). I tried it again by writing everything into a script and using pymol -qc which still ran out of memory. I read somewhere that POVRAY is less of a memory hog so I installed the latest version and simply modified my script to "ray 3600, 3600, renderer=1" to use POVRAY. Everything went smoothly but I noticed that the image generated from POVRAY looked different than the native ray traced structure using PyMOL's ray tracer (simply invoking "ray" without dimensions in PyMOL). Specifically, the light reflections appeared to be dulled in POVRAY and spheres that were further away from the camera view are not distinguishable. I've posted a comparison on the PyMOLWiki:

http://www.pymolwiki.org/index.php/Povray_vs._pymol

Firstly, I apologize as I am completely new to the world of POVRAY and I just assumed that the image produced from either method would give identical/close results but I much prefer the look of the PyMOL ray-tracer. Is there an easy way to set everything up the same way as the PyMOL ray-tracer but for POVRAY? Thank you for your time.

Sean

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[Tsjerk Wassenaar]

Hi Sean,

Unfortunately, getting a good image through POV-Ray requires editing
the POV-Ray file. You can write the scene to disk with the following
commands

pov=open("protein.pov","w")
pov.write(cmd.get_povray()[0])
pov.write("#include \"povray.inc\"")
pov.close()

open("povray.inc","w").write("cmd.get_povray()[1])

Then, take your favorite editor (under windows, you can use the
POV-Ray editor) and make some changes:

1. There's a line starting with #defaults. Remove that and replace it with:

#default {
finish {
ambient .15
diffuse .5
specular 1
roughness .001
reflection { .5 metallic } // Remove this line for less
glossyness and faster tracing
}
}

2. There's a light statement, which says:
light_source{<4000.0001,4000.0001,9960.0000> rgb<1.0,1.0,1.0>}.
Replace it with:

light_source
{
<20,10,0>
rgb 2
area_light <5,5,0>,5,5
adaptive 1
jitter
}

This usually works for me :)

Note that the trace may now take some time. Remove the metallic
reflection for faster tracing.

I hope it helps. POV-Ray is cool, but rather complicated.

Cheers,

Tsjerk

Post by Sean Law
Hi All,
http://www.pymolwiki.org/index.php/Povray_vs._pymol
Firstly, I apologize as I am completely new to the world of POVRAY and I just assumed that the image produced from either method would give identical/close results but I much prefer the look of the PyMOL ray-tracer.  Is there an easy way to set everything up the same way as the PyMOL ray-tracer but for POVRAY?  Thank you for your time.
Sean
________________________________
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]

[Tsjerk Wassenaar]

Hi Sean,

Sorry about that. Tried from the top of my head and the evening had
past too far for that already. These vectors define the directions to
distribute the lights - you basically create an area of light sources.
So you need to set two vectors:

area_light <5,0,0>,<0,5,0>,5,5

This will generate 25 lights in a five by five array perpendicular to
the Pymol viewing axis (which is always along z).

Cheers,

Tsjerk

Tsjerk,
Thanks for the quick response.  I noticed that after "area_light" there
should be two axis vectors (according to the povray website) but you've only
specified one.  Should I just repeat the same axis twice?
Sean

Date: Thu, 14 May 2009 22:47:54 +0200
Subject: Re: [PyMOL] POVRAY Usage
Hi Sean,
Unfortunately, getting a good image through POV-Ray requires editing
the POV-Ray file. You can write the scene to disk with the following
commands
pov=open("protein.pov","w")
pov.write(cmd.get_povray()[0])
pov.write("#include \"povray.inc\"")
pov.close()
open("povray.inc","w").write("cmd.get_povray()[1])
Then, take your favorite editor (under windows, you can use the
#default {
finish {
ambient .15
diffuse .5
specular 1
roughness .001
reflection { .5 metallic } // Remove this line for less
glossyness and faster tracing
}
}
light_source{<4000.0001,4000.0001,9960.0000> rgb<1.0,1.0,1.0>}.
light_source
{
<20,10,0>
rgb 2
area_light <5,5,0>,5,5
adaptive 1
jitter
}
This usually works for me :)
Note that the trace may now take some time. Remove the metallic
reflection for faster tracing.
I hope it helps. POV-Ray is cool, but rather complicated.
Cheers,
Tsjerk

Post by Sean Law
Hi All,
While ray tracing a scene with 10 x-large proteins in grid mode at 3600,
3600 (width, height) I ran out of RAM (2 GB).  I tried it again by writing
everything into a script and using pymol -qc which still ran out of memory.
I read somewhere that POVRAY is less of a memory hog so I installed the
latest version and simply modified my script to "ray 3600, 3600, renderer=1"
to use POVRAY.  Everything went smoothly but I noticed that the image
generated from POVRAY looked different than the native ray traced structure
using PyMOL's ray tracer (simply invoking "ray" without dimensions in
PyMOL).  Specifically, the light reflections appeared to be dulled in POVRAY
and spheres that were further away from the camera view are not
http://www.pymolwiki.org/index.php/Povray_vs._pymol
Firstly, I apologize as I am completely new to the world of POVRAY and I
just assumed that the image produced from either method would give
identical/close results but I much prefer the look of the PyMOL ray-tracer.
Is there an easy way to set everything up the same way as the PyMOL
ray-tracer but for POVRAY?  Thank you for your time.
Sean
________________________________
Help keep personal info safe. Get Internet Explorer 8 today!
------------------------------------------------------------------------------
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production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
_______________________________________________
PyMOL-users mailing list
https://lists.sourceforge.net/lists/listinfo/pymol-users

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]

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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]

[Thomas Stout]

Hi Tsjerk --

What version of PyMOL does this work with? I've been trying your commands with versions 1.1 and 1.2b and while PyMOL reports that the primitives have been processed, nothing is written to the file "protein.pov" other than the header info:

camera {orthographic location <0.0 , 0.0 , 134.1048736572>
look_at <0.0 , 0.0 , -1.0> right -74.9812240601*x up 59.9849815369*y}
#default { finish{phong -1.000 ambient 0.500 diffuse 0.450 phong_size 13
.750000}}
light_source{<4000.0001,4000.0001,9865.8951> rgb<1.0,1.0,1.0>}
plane{z , -206.0869
pigment{color rgb<1.0000,1.0000,1.0000>}
finish{phong 0 specular 0 diffuse 0 ambient 1.0}}
#include "povray.inc"

and povray.inc contains:
cmd.get_povray()[1]

If I save a povray file with the GUI menu selection: File> Save Image As> POV-Ray
then I get everything written to disk. This occurs on both linux and Windows.

Am I missing something that would be more obvious if I had had more coffee today?

Thanks!
-Tom

PS - There was a missing quotation mark:
open("povray.inc","w").write("cmd.get_povray()[1]) -->
open("povray.inc","w").write("cmd.get_povray()[1]")



-----Original Message-----
From: Tsjerk Wassenaar [mailto:***@gmail.com]
Sent: Thu 5/14/2009 1:47 PM
To: Sean Law
Cc: pymol-users
Subject: Re: [PyMOL] POVRAY Usage

Hi Sean,

Unfortunately, getting a good image through POV-Ray requires editing
the POV-Ray file. You can write the scene to disk with the following
commands

pov=open("protein.pov","w")
pov.write(cmd.get_povray()[0])
pov.write("#include \"povray.inc\"")
pov.close()

open("povray.inc","w").write("cmd.get_povray()[1])

Then, take your favorite editor (under windows, you can use the
POV-Ray editor) and make some changes:

1. There's a line starting with #defaults. Remove that and replace it with:

#default {
finish {
ambient .15
diffuse .5
specular 1
roughness .001
reflection { .5 metallic } // Remove this line for less
glossyness and faster tracing
}
}

2. There's a light statement, which says:
light_source{<4000.0001,4000.0001,9960.0000> rgb<1.0,1.0,1.0>}.
Replace it with:

light_source
{
<20,10,0>
rgb 2
area_light <5,5,0>,5,5
adaptive 1
jitter
}

This usually works for me :)

Note that the trace may now take some time. Remove the metallic
reflection for faster tracing.

I hope it helps. POV-Ray is cool, but rather complicated.

Cheers,

Tsjerk

Post by Sean Law
Hi All,
http://www.pymolwiki.org/index.php/Povray_vs._pymol
Firstly, I apologize as I am completely new to the world of POVRAY and I just assumed that the image produced from either method would give identical/close results but I much prefer the look of the PyMOL ray-tracer.  Is there an easy way to set everything up the same way as the PyMOL ray-tracer but for POVRAY?  Thank you for your time.
Sean
________________________________
Help keep personal info safe. Get Internet Explorer 8 today!
------------------------------------------------------------------------------
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
_______________________________________________
PyMOL-users mailing list
https://lists.sourceforge.net/lists/listinfo/pymol-users

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]

------------------------------------------------------------------------------
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
_______________________________________________
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This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

[Robert Campbell]

Hi Tom

Post by Thomas Stout
What version of PyMOL does this work with? I've been trying your commands
with versions 1.1 and 1.2b and while PyMOL reports that the primitives have
been processed, nothing is written to the file "protein.pov" other than the
camera {orthographic location <0.0 , 0.0 , 134.1048736572>
look_at <0.0 , 0.0 , -1.0> right -74.9812240601*x up 59.9849815369*y}
#default { finish{phong -1.000 ambient 0.500 diffuse 0.450
phong_size 13 .750000}}
light_source{<4000.0001,4000.0001,9865.8951> rgb<1.0,1.0,1.0>}
plane{z , -206.0869
pigment{color rgb<1.0000,1.0000,1.0000>}
finish{phong 0 specular 0 diffuse 0 ambient 1.0}}
#include "povray.inc"
cmd.get_povray()[1]
If I save a povray file with the GUI menu selection: File> Save Image As>
POV-Ray then I get everything written to disk. This occurs on both linux
and Windows.
Am I missing something that would be more obvious if I had had more coffee today?
Thanks!
-Tom
open("povray.inc","w").write("cmd.get_povray()[1]) -->
open("povray.inc","w").write("cmd.get_povray()[1]")

I think this is the real key! There was an extra quote. Try:

open("povray.inc","w").write(cmd.get_povray()[1])

Cheers,
Rob

[Tsjerk Wassenaar]

Hi Tom,

Just as Robert says, the quote should be dropped. Maybe you should've
had just one coffee more, but I should also have been more careful
typing. Apparently I usually automatically start of with typing
strings after .write( ;)

Sorry about that.

Tsjerk

Post by Thomas Stout
Hi Tsjerk --
What version of PyMOL does this work with?  I've been trying your commands
with versions 1.1 and 1.2b and while PyMOL reports that the primitives have
been processed, nothing is written to the file "protein.pov" other than the
     camera {orthographic location <0.0 , 0.0 , 134.1048736572>
     look_at  <0.0 , 0.0 , -1.0> right -74.9812240601*x up 59.9849815369*y}
     #default { finish{phong   -1.000 ambient    0.500 diffuse    0.450
phong_size 13
     .750000}}
     light_source{<4000.0001,4000.0001,9865.8951>  rgb<1.0,1.0,1.0>}
     plane{z , -206.0869
      pigment{color rgb<1.0000,1.0000,1.0000>}
      finish{phong 0 specular 0 diffuse 0 ambient 1.0}}
     #include "povray.inc"
     cmd.get_povray()[1]
If I save a povray file with the GUI menu selection: File> Save Image As> POV-Ray
then I get everything written to disk.  This occurs on both linux and
Windows.
Am I missing something that would be more obvious if I had had more coffee today?
Thanks!
-Tom
open("povray.inc","w").write("cmd.get_povray()[1]) -->
open("povray.inc","w").write("cmd.get_povray()[1]")
-----Original Message-----
Sent: Thu 5/14/2009 1:47 PM
To: Sean Law
Cc: pymol-users
Subject: Re: [PyMOL] POVRAY Usage
Hi Sean,
Unfortunately, getting a good image through POV-Ray requires editing
the POV-Ray file. You can write the scene to disk with the following
commands
pov=open("protein.pov","w")
pov.write(cmd.get_povray()[0])
pov.write("#include \"povray.inc\"")
pov.close()
open("povray.inc","w").write("cmd.get_povray()[1])
Then, take your favorite editor (under windows, you can use the
#default {
    finish {
        ambient .15
        diffuse .5
        specular 1
        roughness .001
        reflection { .5 metallic } // Remove this line for less
glossyness and faster tracing
    }
}
light_source{<4000.0001,4000.0001,9960.0000>  rgb<1.0,1.0,1.0>}.
light_source
{
   <20,10,0>
   rgb 2
   area_light <5,5,0>,5,5
   adaptive 1
   jitter
}
This usually works for me :)
Note that the trace may now take some time. Remove the metallic
reflection for faster tracing.
I hope it helps. POV-Ray is cool, but rather complicated.
Cheers,
Tsjerk

Post by Sean Law
Hi All,
While ray tracing a scene with 10 x-large proteins in grid mode at 3600,
3600 (width, height) I ran out of RAM (2 GB).  I tried it again by writing
everything into a script and using pymol -qc which still ran out of memory.
I read somewhere that POVRAY is less of a memory hog so I installed the
latest version and simply modified my script to "ray 3600, 3600, renderer=1"
to use POVRAY.  Everything went smoothly but I noticed that the image
generated from POVRAY looked different than the native ray traced structure
using PyMOL's ray tracer (simply invoking "ray" without dimensions in
PyMOL).  Specifically, the light reflections appeared to be dulled in POVRAY
and spheres that were further away from the camera view are not
http://www.pymolwiki.org/index.php/Povray_vs._pymol
Firstly, I apologize as I am completely new to the world of POVRAY and I
just assumed that the image produced from either method would give
identical/close results but I much prefer the look of the PyMOL ray-tracer.
Is there an easy way to set everything up the same way as the PyMOL
ray-tracer but for POVRAY?  Thank you for your time.
Sean
________________________________
Help keep personal info safe. Get Internet Explorer 8 today!
------------------------------------------------------------------------------
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
_______________________________________________
PyMOL-users mailing list
https://lists.sourceforge.net/lists/listinfo/pymol-users

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]
------------------------------------------------------------------------------
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
_______________________________________________
PyMOL-users mailing list
https://lists.sourceforge.net/lists/listinfo/pymol-users
This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]

[Thomas Stout]

Ah ha! Yes, of course....

Many thanks to you & Rob for catching that!

Note to self: *triple* shots of espresso next time.... :)
-Tom

-----Original Message-----
From: Tsjerk Wassenaar [mailto:***@gmail.com]
Sent: Saturday, May 16, 2009 1:30 AM
To: Thomas Stout
Cc: pymol-users
Subject: Re: [PyMOL] POVRAY Usage

Hi Tom,

Just as Robert says, the quote should be dropped. Maybe you should've had just one coffee more, but I should also have been more careful typing. Apparently I usually automatically start of with typing strings after .write( ;)

Sorry about that.

Tsjerk

Post by Thomas Stout
Hi Tsjerk --
What version of PyMOL does this work with?  I've been trying your
commands with versions 1.1 and 1.2b and while PyMOL reports that the
primitives have been processed, nothing is written to the file
     camera {orthographic location <0.0 , 0.0 , 134.1048736572>
     look_at  <0.0 , 0.0 , -1.0> right -74.9812240601*x up 59.9849815369*y}
     #default { finish{phong   -1.000 ambient    0.500 diffuse   
0.450 phong_size 13
     .750000}}
     light_source{<4000.0001,4000.0001,9865.8951>  rgb<1.0,1.0,1.0>}
     plane{z , -206.0869
      pigment{color rgb<1.0000,1.0000,1.0000>}
      finish{phong 0 specular 0 diffuse 0 ambient 1.0}}
     #include "povray.inc"
     cmd.get_povray()[1]
If I save a povray file with the GUI menu selection: File> Save Image
As> POV-Ray then I get everything written to disk.  This occurs on
both linux and Windows.
Am I missing something that would be more obvious if I had had more coffee today?
Thanks!
-Tom
open("povray.inc","w").write("cmd.get_povray()[1]) -->
open("povray.inc","w").write("cmd.get_povray()[1]")
-----Original Message-----
Sent: Thu 5/14/2009 1:47 PM
To: Sean Law
Cc: pymol-users
Subject: Re: [PyMOL] POVRAY Usage
Hi Sean,
Unfortunately, getting a good image through POV-Ray requires editing
the POV-Ray file. You can write the scene to disk with the following
commands
pov=open("protein.pov","w")
pov.write(cmd.get_povray()[0])
pov.write("#include \"povray.inc\"")
pov.close()
open("povray.inc","w").write("cmd.get_povray()[1])
Then, take your favorite editor (under windows, you can use the
#default {
    finish {
        ambient .15
        diffuse .5
        specular 1
        roughness .001
        reflection { .5 metallic } // Remove this line for less
glossyness and faster tracing
    }
}
light_source{<4000.0001,4000.0001,9960.0000>  rgb<1.0,1.0,1.0>}.
light_source
{
   <20,10,0>
   rgb 2
   area_light <5,5,0>,5,5
   adaptive 1
   jitter
}
This usually works for me :)
Note that the trace may now take some time. Remove the metallic
reflection for faster tracing.
I hope it helps. POV-Ray is cool, but rather complicated.
Cheers,
Tsjerk

Post by Sean Law
Hi All,
While ray tracing a scene with 10 x-large proteins in grid mode at
3600, 3600 (width, height) I ran out of RAM (2 GB).  I tried it again
by writing everything into a script and using pymol -qc which still ran out of memory.
I read somewhere that POVRAY is less of a memory hog so I installed
the latest version and simply modified my script to "ray 3600, 3600, renderer=1"
to use POVRAY.  Everything went smoothly but I noticed that the image
generated from POVRAY looked different than the native ray traced
structure using PyMOL's ray tracer (simply invoking "ray" without
dimensions in PyMOL).  Specifically, the light reflections appeared
to be dulled in POVRAY and spheres that were further away from the
http://www.pymolwiki.org/index.php/Povray_vs._pymol
Firstly, I apologize as I am completely new to the world of POVRAY
and I just assumed that the image produced from either method would
give identical/close results but I much prefer the look of the PyMOL ray-tracer.
Is there an easy way to set everything up the same way as the PyMOL
ray-tracer but for POVRAY?  Thank you for your time.
Sean
________________________________
Help keep personal info safe. Get Internet Explorer 8 today!
---------------------------------------------------------------------
--------- The NEW KODAK i700 Series Scanners deliver under ANY
circumstances! Your production scanning environment may not be a
perfect world - but thanks to Kodak, there's a perfect scanner to get
the job done! With the NEW KODAK i700 Series Scanner you'll get full
speed at 300 dpi even with all image processing features enabled.
http://p.sf.net/sfu/kodak-com
_______________________________________________
PyMOL-users mailing list
https://lists.sourceforge.net/lists/listinfo/pymol-users

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]
----------------------------------------------------------------------
-------- The NEW KODAK i700 Series Scanners deliver under ANY
circumstances! Your production scanning environment may not be a
perfect world - but thanks to Kodak, there's a perfect scanner to get
the job done! With the NEW KODAK i700 Series Scanner you'll get full
speed at 300 dpi even with all image processing features enabled.
http://p.sf.net/sfu/kodak-com
_______________________________________________
PyMOL-users mailing list
https://lists.sourceforge.net/lists/listinfo/pymol-users
This email (including any attachments) may contain material that is
confidential and privileged and is for the sole use of the intended
recipient. Any review, reliance or distribution by others or
forwarding without express permission is strictly prohibited. If you
are not the intended recipient, please contact the sender and delete
all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor and
intercept e-mail messages to and from its systems.

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]
This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.