Re: [PyMOL] Remove me please
Hi Marshall, To unsubscribe you'll have to go to https://lists.sourceforge.net/lists/listinfo/pymol-users and do it yourself. Hope it helps, Tsjerk On Thu, Jun 27, 2013 at 6:00 AM, Pope, Marshall R marshall-p...@uiowa.eduwrote: Warm regards, R. Marshall Pope www.medicine.uiowa.edu/proteomics Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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 jason.vertr...@schrodinger.com
Date: Wednesday, 26 June 2013 21:53
To: Gary Hunter gary.hun...@um.edu.mt
Cc: Thomas Holder thomas.hol...@schrodinger.com,
pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net
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 thomas.hol...@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).
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,
[PyMOL] Pymol DLP 3D
Hello, Does anyone have any experience in running pymol in 3D using a DLP projector? I have an Optoma EW610ST, running from a windows seven machine using a Geforce GT620 GPU. The computer and projector are connected via HDMI but at present I am not able to configure any 3D output. Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.l...@manchester.ac.ukmailto:c.l...@manchester.ac.uk -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Control and shift keys not functioning (Fedora 18)
I've found that all recent versions (1.5, 1.6, non-incentive) of Pymol on my laptop running updated Fedora 18 (nvidia drivers) don't allow me to use the control or shift keys for selection or editing in the gui. I dug out an older version (1.4.1) and it behaved properly. It appears to be pymol specific as coot and other programs work fine. Has anyone seen this before? Thanks, --paul -- Paul Paukstelis, Ph.D Assistant Professor University of Maryland Chemistry Biochemistry Dept. Center for Biomolecular Structure Organization pauks...@umd.edu 301-405-9933 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Anaglyph colours sorted (kind of)
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 jason.vertr...@schrodinger.com
Date: Wednesday, 26 June 2013 21:53
To: Gary Hunter gary.hun...@um.edu.mt
Cc: Thomas Holder thomas.hol...@schrodinger.com,
pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net
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 thomas.hol...@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).
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 (PyMOL-users@lists.sourceforge.net)
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--
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Info Page:
Re: [PyMOL] Anaglyph colours sorted (kind of)
Hi Gary Jason, two more things to add: Optimized anaglyph is not available in immediate mode rendering. You can reset all settings like this: PyMOL reinitialize settings Cheers, Thomas Jason Vertrees wrote, On 06/27/13 15:01: 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 -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
