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 meaning–it 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.


-- Jason


On 18/06/2013 09:59, "Thomas Holder" <thomas.holder@schrodinger.com> 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).
>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.
>  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
>> phone: +356 21316655 (secretary),  Fax: +356 21310577
>> http://www.um.edu.mt/ms/physbiochem
>Thomas Holder
>PyMOL Developer
>Schrödinger Contractor
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