Re: [PyMOL] Anaglyph colours sorted (kind of)

Thanks again for a prompt reply.
 I usually use LCD shutter glasses but they are starting to fail. Anaglyph
is a useful alternative and works on any monitor of course.
I'm also keen to use it for seminars with projected anaglyph images and
movies.
Not sure if I should keep ranting on about anaglyph here? Is the wiki an
alternative?

Just to recap of what to avoid after loading and working on your molecules:
1) do not use a black background
2) do not use "setting > rendering > modernize"
3) be careful with setting quality too high (especially on spheres)

Point 4 should now be:
4) do not use 'ray' when trying to use anaglyph stereo. This is a shame
because an anaglyph image for a slide or printout might be useful.

Some irreversible colour changes are frustrating after working for hours on
molecular structures, and then finding anaglyph does not work. That¹s why
I'd like to find a 'reset' command for the settings ­ edit all settings.
Initialise wipes out all my hard work (molecules, objects, selections, maps,
etc etc). Currently I just have to revert to the last saved pse file.

Any idea why using modern shaders does not work with anaglyph and might this
be improved later?

Gary





 Prof. Gary J. Hunter,
 Department of Physiology and Biochemistry
 University of Malta, Msida, MSD 2080, Malta.
 phone: +356 2340 2917
 phone: +356 21316655 (secretary),  Fax: +356 21310577
 http://www.um.edu.mt/ms/physbiochem

From:  Jason Vertrees <jas...@sc...>
Date:  Wednesday, 26 June 2013 21:53
To:  Gary Hunter <gar...@um...>
Cc:  Thomas Holder <tho...@sc...>,
"pym...@li..." <pym...@li...>
Subject:  Re: [PyMOL] Anaglyph colours sorted (kind of)

Hi Gary,


> 1) do not use a black background

Agreed. Something like gray works well in my experience. Don't forget in
techniques like anaglyph and chromadepth color takes on another meaning­it
encodes depth or separation. It's useful to keep this in mind.

 
> 2) do not use "setting > rendering > modernize"

If you have a modern video card that supports shaders well, Setting >
Rendering > Modernize will give you better performance and much prettier
graphics. If, however, you're on a laptop with an old Intel graphics card,
stick to immediate mode rendering ('set use_shaders, 0').

 
> 3) be careful with setting quality too high (especially on spheres)

Again, using Setting > Rendering > Modernize will actually give you pixel
perfect spheres drawn quickly. But, in immediate mode, you are correct.


To create the highest-quality movies or images, make sure you ray trace your
images. This can be done with the 'ray', and 'png' commands or as movie
creation time if 'ray_trace_frames' is set.


To reinitialize PyMOL just run the "reinitialize" command.

Cheers,

-- Jason

 
> 
> On 18/06/2013 09:59, "Thomas Holder" <tho...@sc...> wrote:
> 
>> >Hi Gary,
>> >
>> >actually PyMOL should be optimized for red/cyan and not green/magenta.
>> >There is no option to change the colors, sorry.
>> >
>> >In PyMOL 1.5 anaglyph has been improved and there are is an
>> >"anaglyph_mode" settings which defaults to 4 ("optimized anaglyph").
>> >Other reasonable values are 3 ("half-color") and 1 (gray).
>> >
>> >http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
>> >
>> >If you really need to change the colors, you could take the open-source
>> >code and tweak the anaglyph_mode matrix in layer1/Scene.c
>> >
>> >Hope that helps.
>> >
>> >Cheers,
>> >  Thomas
>> >
>> >Gary Hunter wrote, On 06/17/13 09:53:
>>> >> Is there a way to customise the colours used in anaglyph stereo mode?
>>> >> Anaglyph mode has been optimised for green/magenta glasses but I have
>>> >> lots of red/cyan ones so I'd like to change the colours used if I can.
>>> >> Gary
>>> >>
>>> >> Prof. Gary J. Hunter,
>>> >> Department of Physiology and Biochemistry
>>> >> University of Malta, Msida, MSD 2080, Malta.
>>> >> phone: +356 2340 2917 <tel:%2B356%202340%202917>
>>> >> phone: +356 21316655 <tel:%2B356%2021316655>  (secretary),  Fax: +356
>>> 21310577 <tel:%2B356%2021310577>
>>> >> http://www.um.edu.mt/ms/physbiochem
>> >
>> >--
>> >Thomas Holder
>> >PyMOL Developer
>> >Schrödinger Contractor
>> >
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-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120