[PyMOL] Getting rid of shadows

[Vivien Schoonenberg]

Hi,

 

I'm recoloring my protein in different shades of similar colors, but to
truly see the difference between them, I want to create a view in pyMOL
without any shadows.

For this purpose, I want to make a half sphere behind the camera with
lights, which all emit the same amount of light. I have a hard time figuring
out how to set coordinates and changing the strength of the lights. Do you
maybe have a suggestion on how to solve this?

 

Thanks,

Vivien

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Re: [PyMOL] Getting rid of shadows

[Rui Sousa]

Hi Vivian,

I'm not sure if I fully understand your question, but if you want to 
have a picture without shadows, by using "set light_count, 0" 
(https://pymolwiki.org/index.php/Light_count) you should be able to 
achieve this.


Rui

Le 22/02/2017 17:46, Vivien Schoonenberg a écrit :


Hi,

I’m recoloring my protein in different shades of similar colors, but 
to truly see the difference between them, I want to create a view in 
pyMOL without any shadows.


For this purpose, I want to make a half sphere behind the camera with 
lights, which all emit the same amount of light. I have a hard time 
figuring out how to set coordinates and changing the strength of the 
lights. Do you maybe have a suggestion on how to solve this?


Thanks,

Vivien



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Re: [PyMOL] Getting rid of shadows

[Vivien Schoonenberg]

Hi Rui,

 

Thank you!

I also already figured out that if I turn off the depth cue most of my
problem is solved as well ( “set depth_cue, 0”)

 

-Vivien

 

From: Rui Sousa [mailto:rui.so...@univ-nantes.fr] 
Sent: Thursday, February 23, 2017 10:02
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Getting rid of shadows

 

Hi Vivian,

I'm not sure if I fully understand your question, but if you want to have a
picture without shadows, by using "set light_count, 0"
(https://pymolwiki.org/index.php/Light_count) you should be able to achieve
this.

Rui

Le 22/02/2017 17:46, Vivien Schoonenberg a écrit :

Hi,

 

I’m recoloring my protein in different shades of similar colors, but to
truly see the difference between them, I want to create a view in pyMOL
without any shadows.

For this purpose, I want to make a half sphere behind the camera with
lights, which all emit the same amount of light. I have a hard time figuring
out how to set coordinates and changing the strength of the lights. Do you
maybe have a suggestion on how to solve this?

 

Thanks,

Vivien







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 )
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[PyMOL] Antwort: course or tutorial to make nice pictures

[honegger]

Hi Clarissa

I have just deposited the slides to my 1.5 day class on macromolecular 
visualization on Research Gate

https://www.researchgate.net/publication/313877004_Introduction_to_PyMOL
https://www.researchgate.net/publication/313877009_Intermediate_PyMOL
https://www.researchgate.net/publication/313877075_Advanced_PyMOL

best regards
Annemarie


Message: 1
Date: Wed, 15 Feb 2017 10:44:59 -0300
From: Clarisa Alvarez 
Subject: [PyMOL] course or tutorial to make nice pictures
To: pymol-users@lists.sourceforge.net
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hi! Do anyone know any course or tutorial to make nice images with pymol. I
have already done basic tutorials but I would like to learn a little more.
Thanks in advance.
Clarisa.
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[PyMOL] Antwort: PyMOL-users Digest, Vol 129, Issue 9

[honegger]

Dear Vivian

If you just want to get rid of shadows in exported ray-traced images, you can 
specify
set ray_shadows, 0 (https://pymolwiki.org/index.php/Ray_shadow)

set depth_cue,0 (https://pymolwiki.org/index.php/Depth_cue)
will get rid of the color modulation due to dept cueing

Annemarie


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Message: 5
Date: Wed, 22 Feb 2017 11:46:02 -0500
From: "Vivien Schoonenberg" 
Subject: [PyMOL] Getting rid of shadows
To: 
Message-ID: <001201d28d2b$27a06960$76e13c20$@gmail.com>
Content-Type: text/plain; charset="us-ascii"

Hi,

 

I'm recoloring my protein in different shades of similar colors, but to
truly see the difference between them, I want to create a view in pyMOL
without any shadows.

For this purpose, I want to make a half sphere behind the camera with
lights, which all emit the same amount of light. I have a hard time figuring
out how to set coordinates and changing the strength of the lights. Do you
maybe have a suggestion on how to solve this?

 

Thanks,

Vivien


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Re: [PyMOL] Getting rid of shadows

[Roger Rowlett]

One option is to turn off shadows:

set ray_shadow, off

Will that work for you?

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On 2/22/2017 11:46 AM, Vivien Schoonenberg wrote:


Hi,

I’m recoloring my protein in different shades of similar colors, but 
to truly see the difference between them, I want to create a view in 
pyMOL without any shadows.


For this purpose, I want to make a half sphere behind the camera with 
lights, which all emit the same amount of light. I have a hard time 
figuring out how to set coordinates and changing the strength of the 
lights. Do you maybe have a suggestion on how to solve this?


Thanks,

Vivien



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[PyMOL] Disable ray tracing in script for volumes

[Thomas Grant]

Dear all,

I've written a .pml script to render volumes and save png files. The script
works fine when running it from the GUI, but for some reason when I run in
command line mode with pymol -cqr myscript.pml the image saved is blank.

It appears that when running from the command line it automatically ray
traces the image, even when I set ray = 0 in the png command, and since
volumes don't work well with ray tracing, the images end up blank.

I tried setting ray_volume=1, but that still doesn't fix the problem.

My script is below, as is the output from the command line and from the
GUI.  Notice that when running from the command line there is a "Ray:
render time:" line that doesn't appear when running from the GUI.

Thanks for any insight.

Tom

*myscript.pml:*

$>cat myscript.pml:

bg white

fetch 1oky, type=2fofc, async=0

volume 1okyVol, 1oky_2fofc

set ray_volume, 1

png volume.png, ray=0


*command line output (doesn't work):*

$>pymol -cqr myscript.pml:

PyMOL>bg white

PyMOL>fetch 1oky, type=2fofc, async=0

 ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'.

 BRIXStrToMap: Map Size 102 x 99 x 92

 BRIXStrToMap: Range = -0.906629 to 2.095844

 BRIXStrToMap: Calculated Mean =   -0.006, Sigma =0.251

 BRIXStrToMap: Normalizing...

 Crystal: Unit Cell  124.162  124.162   47.300

 Crystal: Alpha Beta Gamma90.000   90.000  120.000

 Crystal: RealToFrac Matrix

 Crystal:0.00810.0046   -0.

 Crystal:0.0.0093   -0.

 Crystal:0.0.0.0211

 Crystal: FracToReal Matrix

 Crystal:  124.1625  -62.08120.

 Crystal:0.  107.52790.

 Crystal:0.0.   47.3000

 Crystal: Unit Cell Volume   631499.

 CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc".

PyMOL>volume 1okyVol, 1oky_2fofc

 Executive: object "1okyVol" created.

 Volume: created "1okyVol"

PyMOL>set ray_volume, 1

 Setting: ray_volume set to on.

PyMOL>png volume.png, ray=0

 Ray: render time: 0.01 sec. = 242165.4 frames/hour (0.01 sec. accum.).

 ScenePNG: wrote 640x480 pixel image to file "volume.png".

*GUI output (works):*
$>pymol -qr myscript.pml:

 Detected OpenGL version 2.0 or greater. Shaders available.

 Detected GLSL version 1.20.

PyMOL>bg white

PyMOL>fetch 1oky, type=2fofc, async=0

 ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'.

 BRIXStrToMap: Map Size 102 x 99 x 92

 BRIXStrToMap: Range = -0.906629 to 2.095844

 BRIXStrToMap: Calculated Mean =   -0.006, Sigma =0.251

 BRIXStrToMap: Normalizing...

 Crystal: Unit Cell  124.162  124.162   47.300

 Crystal: Alpha Beta Gamma90.000   90.000  120.000

 Crystal: RealToFrac Matrix

 Crystal:0.00810.0046   -0.

 Crystal:0.0.0093   -0.

 Crystal:0.0.0.0211

 Crystal: FracToReal Matrix

 Crystal:  124.1625  -62.08120.

 Crystal:0.  107.52790.

 Crystal:0.0.   47.3000

 Crystal: Unit Cell Volume   631499.

 CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc".

PyMOL>volume 1okyVol, 1oky_2fofc

 Executive: object "1okyVol" created.

 Volume: created "1okyVol"

PyMOL>set ray_volume, 1

 Setting: ray_volume set to on.

PyMOL>png volume.png, ray=0

 ScenePNG: wrote 640x480 pixel image to file "volume.png".




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