PyMOL Molecular Graphics System

On Monday, April 26, 2004, at 04:19  PM, <pdoucett@...> wrote:

> Hello Pymoliacs,
>
> I have been playing around with the lighting and gamma settings, but 
> can
> never get a true black. The black always shows up as grey. Does anyone 
> know
> how to get black to be black?
>
> Pete D.
> UCLA Chemistry
>
>

Hi Pete -

If what you want is a "flat black", i.e. just a silhouette of the 
ribbon/surface/whatever, then set the color to black and turn the 
specular reflections off ("set specular, 0").  This certainly looks 
like rgb 0,0,0 to me (MacPymol v.0.94, OS X 10.2.8) and is completely 
invisible in front of a black background.  If you're looking for a 
black with some texture visible, then you will get some gr(e/a)y in 
with your black...

Hope this helps,

Matt

-- 
Matthew Franklin            Phone:(650)225-4596
Postdoctoral Researcher       Fax:(650)225-3734
Genentech, Inc.
1 DNA Way, South San Francisco, CA 94080

Hello Matt,

Thanks for the suggestion. Unfortunately this still gives me a very light 
grey--nowhere near what you are seeing on your machine. The molecule is 
*clearly* visible against the black background. I am using pymol on win XP. I 
think I will put pymol on my linux machine and see if that makes a difference.

Pete


Matt Franklin <franklin.matt@...> said:

> 
> On Monday, April 26, 2004, at 04:19  PM, <pdoucett@...> wrote:
> 
> > Hello Pymoliacs,
> >
> > I have been playing around with the lighting and gamma settings, but 
> > can
> > never get a true black. The black always shows up as grey. Does anyone 
> > know
> > how to get black to be black?
> >
> > Pete D.
> > UCLA Chemistry
> >
> >
> 
> Hi Pete -
> 
> If what you want is a "flat black", i.e. just a silhouette of the 
> ribbon/surface/whatever, then set the color to black and turn the 
> specular reflections off ("set specular, 0").  This certainly looks 
> like rgb 0,0,0 to me (MacPymol v.0.94, OS X 10.2.8) and is completely 
> invisible in front of a black background.  If you're looking for a 
> black with some texture visible, then you will get some gr(e/a)y in 
> with your black...
> 
> Hope this helps,
> 
> Matt
> 
> -- 
> Matthew Franklin            Phone:(650)225-4596
> Postdoctoral Researcher       Fax:(650)225-3734
> Genentech, Inc.
> 1 DNA Way, South San Francisco, CA 94080
> 



--

On Tue, 2004-04-27 at 17:27, pdoucett@... wrote:

> Thanks for the suggestion. Unfortunately this still gives me a very light 
> grey--nowhere near what you are seeing on your machine. The molecule is 
> *clearly* visible against the black background. I am using pymol on win XP. I 
> think I will put pymol on my linux machine and see if that makes a difference.


Pete-

I assume that what you're seeing is the result of minute scattering
during ray tracing (Warren- is this correct?). That's just a guess.

Whatever the cause, you might consider using an image editor like the
gimp (see * below; or Photoshop on Windows, I guess) to select all
pixels within some distance of black and recoloring those as exactly
black. For a neater effect, you could add an alpha channel and make the
pixels transparent, in which case your ray traced image would appear to
"float" on whatever background you used.

Come to think of it, perhaps this would make a useful setting in PyMOL
itself (unless it already exists and I just haven't come across it): a
flatten_background setting (a rgb distance) which would cause any pixel
within the that distance of the background color to be set exactly to
the background color. If background color were extended to include an
alpha channel, then this idea would also provide for transparent
backgrounds.

-Reece

* If you're using gimp, do this: load the png, add an alpha channel
(Image > Alpha > Add Alpha Channel), then select by color (Select > By
Color..., then click black somewhere), then either 1) fill with the
bucket to set the color or 2) cut the selection to make it transparent.

-- 
Reece Hart, Ph.D.                       rkh@..., http://www.gene.com/
Genentech, Inc.                         650-225-6133 (voice), -5389 (fax)
Bioinformatics and Protein Engineering
1 DNA Way, MS-93                        http://www.in-machina.com/~reece/
South San Francisco, CA  94080-4990     reece@..., GPG: 0x25EC91A0

Reece,

PyMOL already has full alpha support for transparency and backgrounds.

To get that floating effect in PowerPoint, Photoshop, or Keynote:

set ray_opaque_background, off
ray
png my_alpha_image.png

That's one of the reasons I like PNG format, but beware of using transparent
images in web pages:  Most current Windows versions of IE don't have alpha
channel support with PNG files (or any 32-bit image format AFAIK).

Cheers,
Warren


--
mailto:warren@...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pymol-users-admin@... 
> [mailto:pymol-users-admin@...] On Behalf Of 
> Reece Hart
> Sent: Tuesday, April 27, 2004 8:54 PM
> To: pymol-users@...
> Subject: Re: [PyMOL] True Black?
> 
> On Tue, 2004-04-27 at 17:27, pdoucett@... wrote: 
> 
> 	Thanks for the suggestion. Unfortunately this still 
> gives me a very light 
> 	grey--nowhere near what you are seeing on your machine. 
> The molecule is 
> 	*clearly* visible against the black background. I am 
> using pymol on win XP. I 
> 	think I will put pymol on my linux machine and see if 
> that makes a difference.
> 
> 
> Pete-
> 
> I assume that what you're seeing is the result of minute 
> scattering during ray tracing (Warren- is this correct?). 
> That's just a guess.
> 
> Whatever the cause, you might consider using an image editor 
> like the gimp <http://www.gimp.org/>  (see * below; or 
> Photoshop on Windows, I guess) to select all pixels within 
> some distance of black and recoloring those as exactly black. 
> For a neater effect, you could add an alpha channel and make 
> the pixels transparent, in which case your ray traced image 
> would appear to "float" on whatever background you used.
> 
> Come to think of it, perhaps this would make a useful setting 
> in PyMOL itself (unless it already exists and I just haven't 
> come across it): a flatten_background setting (a rgb 
> distance) which would cause any pixel within the that 
> distance of the background color to be set exactly to the 
> background color. If background color were extended to 
> include an alpha channel, then this idea would also provide 
> for transparent backgrounds.
> 
> -Reece
> 
> * If you're using gimp, do this: load the png, add an alpha 
> channel (Image > Alpha > Add Alpha Channel), then select by 
> color (Select > By Color..., then click black somewhere), 
> then either 1) fill with the bucket to set the color or 2) 
> cut the selection to make it transparent. 
> 
> 
> 
> 
> -- 
> Reece Hart, Ph.D.                       rkh@..., 
> http://www.gene.com/
> Genentech, Inc.                         650-225-6133 (voice), 
> -5389 (fax)
> Bioinformatics and Protein Engineering
> 1 DNA Way, MS-93                        
> http://www.in-machina.com/~reece/
> South San Francisco, CA  94080-4990     reece@..., 
> GPG: 0x25EC91A0
> <http://www.gimp.org/> 
>