Re: [PyMOL] Producing publication quality images

[Mark A Saper]

You can easily change the resolution (dpi) of an image without  
changing the number of pixels, by editing the file in Photoshop (in  
Image Size, change resolution without rescaling) or in  
GraphicConverter (on Mac).

_
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
930 N University Ave
Ann Arbor MI 48109-1055   U.S.A.

sa...@umich.edu(734) 764-3353fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

RE: [PyMOL] Producing publication quality images

[Michael George Lerner]

It's not pretty, and this is easy enough to do by hand, but I've had 
enough people ask me about this that I hacked up a little rendering plugin 
just now.  Can someone grab it from


http://www-personal.umich.edu/~mlerner/PyMOL/rendering.py

put it in $PYMOL_PATH/modules/pmg_tk/startup/ (or whatever it is you do on 
your OS of choice) and tell me what you think?


-michael

--
www.umich.edu/~mlerner |_  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|   / \ | mler...@umich

On Tue, 21 Mar 2006, Warren DeLano wrote:


Terry,

The trick is to render large and then reduce.  With recent versions, you
can do something like this

# To get a 300 dpi PNG file for a 4 inch by 3 inch image...

# Ray-traced:

ray 1200,900
png hires_ray.pdb, dpi=300

# OpenGL:

draw 1200,900
png hires_ogl.pdb, dpi=300

Cheers,
Warren

--
Warren L. DeLano, Ph.D.
Principal Scientist

. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942  Tech:(650)-872-0834
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com



-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Terry Jones
Sent: Tuesday, March 21, 2006 12:43 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Producing publication quality images

Hi. I'm wondering if there's a way to make pymol produce
high-quality images suitable for publication.

I've used ray/png to produce images, but the person I pass
them on to tells me they're only 50 to 100 dpi, and they're
wanting 300 dpi if possible.

Is there a way to do this in pymol? Or can I export image
data and use some other tools to get to a 300dpi image?

BTW, I'll try to make sure that pymol gets credited in the paper.

Thanks,
Terry


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Re: [PyMOL] stereo: should wait for LCD solutions in near future?

[Ricardo Aparicio]

Warren,

Thank you for replying.

Cheers,

Ricardo


Warren DeLano wrote:


Ricardo,

A 20+" 1600-1920 by 1200 pixel "switchable" stereo LCD display based on
Parallax Barrier at a $2-3,000 price point would have a good shot at
displacing shutter glasses -- but I don't know that any such product yet
exists.  


In my experience:

- Lenticular displays work fine for video but are unsuitable for
technical graphics where thin lines must be rendered cleanly and without
artifacts or anisotropy.

- Polarization and/or mirror-based displays are too bulky, complex, and
expensive.

- Only Parallax Barrier provides both stereo and non-stereo display
modes in the space of a desktop LCD monitor without unreasonable visual
artifacts.  But losing 2X in horizontal resolution means one needs to
start with a very high resolution display (1920 or higher).  The $500
Sharp 3D autostereoscopic display is a great proof of concept, and if it
had 3X more pixels, I think it would be a viable option.  


Incidentally, Dimension Technologies has a 19" autostereoscopic display
for $3,695 with about twice as many pixels as the Sharp 15"
, but I think it
will still take 50% more pixels for ~33% less money in order to tap the
full potential of this market. 


For now, I'd stick with CRTs and shutter glasses.

Cheers,
Warren

--
Warren L. DeLano, Ph.D. 
Principal Scientist


. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  



 


-Original Message-
From: pymol-users-ad...@lists.sourceforge.net 
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
Ricardo Aparicio

Sent: Monday, March 20, 2006 2:17 PM
To: pymol-us...@lists.sf.net
Subject: [PyMOL] stereo: should wait for LCD solutions in near future?

Dear all,

After reading many messages from last January, I would like 
to have a better idea if the best option for stereo continues 
to be the one kindly indicated  at  
http://pymol.sourceforge.net/stereo3d.html

(some messages mentioned alternatives like those listed bellow).

Is there a chance that in near future a technology based on 
LCD monitors may become available at reasonable price and 
competitive image quality?
(intrinsic horizontal low resolution of LCD 3D options seems 
to be a problem)


Comments are welcomed.

Cheers,

Ricardo Aparicio


http://store.sharpsystems.com/product.asp?sku=2555920
http://www.sharp3d.com/technology/howsharp3dworks/

http://www.inition.co.uk/inition/open_week_stereoscopic.htm
http://www.inition.co.uk/inition/compare.php?SubCatID=1
http://www.inition.co.uk/inition/product.php?URL_=product_ster
eovis_planar_sd1710&SubCatID_=3


http://www.crystalcanyons.net/abouts/3dc9_DualMonitorComplete.shtm






   




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.

 

RE: [PyMOL] Producing publication quality images

[Terry Jones]

Thanks Warren, I'll try that. I got two other replies, neither mentioning
the 300dpi arg to png. If that isn't recognized, I'll upgrade.

Terry

RE: [PyMOL] Producing publication quality images

[Warren DeLano]

Terry,

The trick is to render large and then reduce.  With recent versions, you
can do something like this

# To get a 300 dpi PNG file for a 4 inch by 3 inch image...

# Ray-traced:

ray 1200,900
png hires_ray.pdb, dpi=300

# OpenGL:

draw 1200,900
png hires_ogl.pdb, dpi=300

Cheers,
Warren

--
Warren L. DeLano, Ph.D. 
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  
 

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Terry Jones
> Sent: Tuesday, March 21, 2006 12:43 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Producing publication quality images
> 
> Hi. I'm wondering if there's a way to make pymol produce 
> high-quality images suitable for publication.
> 
> I've used ray/png to produce images, but the person I pass 
> them on to tells me they're only 50 to 100 dpi, and they're 
> wanting 300 dpi if possible.
> 
> Is there a way to do this in pymol? Or can I export image 
> data and use some other tools to get to a 300dpi image?
> 
> BTW, I'll try to make sure that pymol gets credited in the paper.
> 
> Thanks,
> Terry
> 
> 
> ---
> This SF.Net email is sponsored by xPML, a groundbreaking 
> scripting language that extends applications into web and 
> mobile media. Attend the live webcast and join the prime 
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&;
> dat=121642
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 
> 

[PyMOL] Producing publication quality images

[Terry Jones]

Hi. I'm wondering if there's a way to make pymol produce high-quality
images suitable for publication.

I've used ray/png to produce images, but the person I pass them on to tells
me they're only 50 to 100 dpi, and they're wanting 300 dpi if possible.

Is there a way to do this in pymol? Or can I export image data and use some
other tools to get to a 300dpi image?

BTW, I'll try to make sure that pymol gets credited in the paper.

Thanks,
Terry

[PyMOL] Red-Blue anaglyph in Pymol

[Jean-Christophe AME]

Hello,

I was wondering if it is possible to produce Red-Blue Anaglyph using  
pymol either in "live" or static. I saw a demo site of pymol where it  
seems to be possible (http://www.sciencesoft.at/index.jsp? 
link=pymol&lang=en), but how ? Or is it planned for a next version of  
Pymol.

Thanks.
Jean-Christophe


Jean-Christophe Amé, PhD
Département Intégrité du Génome, UMR 7175-LC1 du CNRS
École Supérieure de Biotechnologie de Strasbourg
Pôle API
Parc d'innovation, Boulevard Sébastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: +33 (0)3 90 24 47 05
Fax.: +33 (0)3 90 24 46 86

http://parplink.u-strasbg.fr
http://idg.u-strasbg.fr/

« Science sans conscience n'est que ruine de l'âme ...» (François  
Rabelais, 1483-1553)