From: Jason V. <jas...@sc...> - 2013-06-27 13:02:27
|
Hi Gary, I think you misunderstood. First, with a good video card, use Setting > Rendering > Modernize for the fastest and highest quality on screen rendering. In fact, it's essentially as good as ray tracing but without shadows. If your machine cannot handle this, the fallback is immediate mode rendering, which PyMOL has been using for years. Machines with older and lower quality video cards sometimes cannot handle this rendering technique: they're simply incapable of using such drawing techniques. > 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. You have this backwards. The 'ray' command works just fine in anaglyph mode. I've made countless 3D images using 'ray' and anaglyph mode. > Some irreversible colour changes are frustrating after working for hours on molecular structures, and then finding anaglyph does not work. That’s 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. Since we do not have 'undo' for things like colors you have to save keep saving your session files so you don't lose any color changes. > Any idea why using modern shaders does not work with anaglyph and might this be improved later? Again, modern shaders do indeed work with PyMOL–I use them all the time–your video card just has to be good enough and you need to be using PyMOL v1.5 or later. Cheers, -- Jason > 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 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. > > 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 >> >> phone: +356 21316655 (secretary), Fax: +356 21310577 >> >> http://www.um.edu.mt/ms/physbiochem >> > >> >-- >> >Thomas Holder >> >PyMOL Developer >> >Schrödinger Contractor >> > >> >-------------------------------------------------------------------------- >> >---- >> >This SF.net email is sponsored by Windows: >> > >> >Build for Windows Store. >> > >> >http://p.sf.net/sfu/windows-dev2dev >> >_______________________________________________ >> >PyMOL-users mailing list (PyM...@li...) >> >Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >Archives: http://www.mail-archive.com/pym...@li... >> > >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) Jas...@sc... > (o) +1 (603) 374-7120 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |