Hi Gary,
Stereo has not been dropped, it should work with PyMOL 2.x on Windows and
Linux. Does PyMOL report "quad-buffer stereo 3D detected and enabled" on
startup? Does it work if you run "pymol -S" (or "pymolwin +2 -S") from a
command prompt?
Cheers,
Thomas
> On May 10, 2019, at 1:55 PM,
christopher.colb...@ndsu.edu>>
Subject: Re: [PyMOL] Stereo Set up with PyMOL v1.7.4.4 EDU
Dear Chris,
We have a similar setup using an older Quadro card employing a dual screen
output (one DP/DVI-port for each projector). The two "screens" are in "clone
mode"
Dear Chris,
We have a similar setup using an older Quadro card employing a dual
screen output (one DP/DVI-port for each projector). The two "screens"
are in "clone mode" (NVIDIA control panel), as described e.h. here:
http://nvidia.custhelp.com/app/answers/detail/a_id/3012/~/how-to-configure
On 01-Jun-2015 01:43, EPF (Esben Peter Friis) wrote:
> If you need stereo-in-a-window, you must have a Quadro card.
And not just _any_ Quadro card. Nvidia periodically desupports stereo
on older model Quadros. We had a bunch of machines with Quadro FX 1400
cards stuck at an old Nvidia driver a
Hi Gary
GeForce cards do support Nvidia 3D vision 2 under Windows, but in full screen
only. (Tested with Windows 8, PyMOL and an Alienware 3D-capable laptop).
If you need stereo-in-a-window, you must have a Quadro card.
It works with Yasara too (full screen), but for unknown reasons, the stereo
On 15/07/13 18:56, Thomas Holder wrote:
> Hi Justin,
>
> we fixed this in sourceforge SVN today. Please recompile and check if it
> works for you. Thanks.
>
> Cheers,
> Thomas
Thanks Thomas,
works perfectly now!
Cheers,
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural
Hi Justin,
we fixed this in sourceforge SVN today. Please recompile and check if it
works for you. Thanks.
Cheers,
Thomas
Justin Lecher wrote, On 07/15/13 13:32:
> Hi,
>
> Static objects like the sidebar and the sequence are only rendered for
> one eye. This results in some unpleasant optical
Hi Yamei,
There's nothing wrong with your approach. If you like the results, and
they illustrate the point your trying to make, it's good.
Cheers,
Tsjerk
On Thu, Feb 21, 2013 at 9:22 AM, Yamei Yu wrote:
> Hi All,
>
> I want to generate a stereo image for a structure. I use
> pymol-diaplay-Ster
Harry,
I have not seen any evidence of the NVidia 3D NVision system working
on a modern Mac OS X system. For the Mac, you'll have to use something
passive like Zalman (or maybe the new anaglyph).
Cheers,
-- Jason
On Tue, Mar 20, 2012 at 3:59 AM, Harry Mark Greenblatt
wrote:
> BS"D
>
> Dear All
Chris,
I don't know much about MACs, but on Linux you can have a look at
/var/log/xorg.?.log or some similar log file. Take a look at the
equivalent log file. May be there is some clue as to why the emitter
won't work. Looks to me like a driver issue.
Good luck,
Carsten
> -Original
On Mon, Jun 14, 2010 at 06:45:10PM +0200, Dirk Kostrewa wrote:
> For the MacPyMOL version, the "-S" flag is _not_ necessary for
> quad-buffered stereo, if you go to the monitor settings and drag the
> menu bar in the monitor arrangement settings to the CRT screen, _prior_
> to invoking MacPyMOL
Hi Patrick and Ben,
Am 14.06.10 18:15, schrieb Ben Eisenbraun:
> Hi Patrick,
>
>
>> I invoke the stereo version with this command:
>>
>> /Applications/PyMol/MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1250 -Y 100 -S
>>
>> The X/Y placement is to ensure that the window falls on my CRT, and the
>
Hi Patrick,
> I invoke the stereo version with this command:
>
> /Applications/PyMol/MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1250 -Y 100 -S
>
> The X/Y placement is to ensure that the window falls on my CRT, and the
> -S seems to be necessary to force stereo (if I just run regular MacPyMOL,
>
OK, this is weird. When I upgraded to Snow Leopard a month or two ago, I saw
the exact same phenomenon that Ben describes (but stereo continued to work fine
in Coot). I was too busy to follow it up, however.
This morning, prompted by Ben, I tried again, and lo and behold stereo in
MacPyMOL wor
Norbert,
Try something like this for a side-by-side stereo image:
turn y,3
draw
png left_image.png
turn y, -6
draw
png right_image.png
turn y,3
Caveat is that potential shadows may not be rendered correctly in stereo.
That's why the angle option was implemented in ray.
HTH
Carsten
Oww, that hurts! I knew it should be somewhere, but it was right there
with the 'png' command: the dpi setting:
png image.png, dpi=300
So, no need to edit anything afterwards...
Cheers,
Tsjerk
On Sun, Oct 11, 2009 at 11:31 AM, Tsjerk Wassenaar wrote:
> Hey :)
>
> Why revert to powerpoint and
Hey :)
Why revert to powerpoint and or photoshop? First of all, it's not the
image resolution (dpi) that counts, it's the number of pixels, the
geometry. That you can give as argument to ray. Second, if you want a
distance between images of 63 mm, you seem to want a total image
length of 126 mm, w
Hi Peter,
I usually assemble stereo images in Photoshop and stay away from PowerPoint.
However, check out the following link that shows you how to save images in
hi-res in PowerPoint:
http://www.motifolio.com/tips2.html
If you write out the images in PowerPoint with the resolution you want you
wa [mailto:kostr...@genzentrum.lmu.de]
Sent: Monday, September 28, 2009 7:26 AM
To: PyMOLBB
Cc: CCP4BB
Subject: Re: [PyMOL] Stereo flipping in coot and pymol
Dear Joachim,
you don't say whether its Linux, Windows or Mac OS X and which emitter
and glasses you are using. I've seen this behavio
Dear Joachim,
you don't say whether its Linux, Windows or Mac OS X and which emitter
and glasses you are using. I've seen this behaviour long time ago with
very old Nvidia graphics card drivers under Linux. Sometimes, I still
see this behaviour with new drivers but with old computer hardwar
Frank,
Honestly, this is the job of the underlying graphics driver, and I suspect
that nVidia will soon support interleaved stereo 3D via the standard OpenGL
quadbuffer API. They've shown a willingness to support quite a number of
different approaches already.
However, I amm wary of checkerboard
Patrick,
Please use the Display panel in System Preferences to confirm that the CRT
monitor is configured for a high refresh rate (100 Hz or better). By
default, MacPyMOL won't open a stereo context if the refresh rate is too
low.
However, you can indeed force use of a stereo context with the
Frank,
We no longer have access to Sharp3D equipment, but here is the last PyMOL
build known to work with that monitor: http://delsci.com/sharp3d/
The general feedback from from demos was that these small low-resolution
monitors are not sufficient to meet molecular graphics needs. However, th
Hi All
The Xorg >< Stereo problem might also be related to the driver
versions of NVIDIA with new distributions. FX cards seem to be fine
with 8xxx series of driver, while stereo might not work with quadro 4
cards (980XGL and similar). Theres a thread at nvnews with some info
and a patch to make
Hi Hasan,
Have a look at "label"... (and read the manual :))
Cheers,
Tsjerk
On 7/27/06, Demirci, Hasan wrote:
I have a cross-eye stereo image generated by PYMOL. Is there an easy way of
custom labeling the residues by using PYMOL ?
Or should I use a photo editor program to label everything
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 ye
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
Bill,
> Does anyone know if the new intel min-macs support stereo...
Unlikely -- the new Mini's have Intel GMA950 Graphics Processor and there is no
upgrade available. In the PC world, Intel-based OpenGL systems are plagued by
poor performance and compatibility problems. It would surprise me
> Does this mean that until Apple release an OS / OpenGL driver
> upgrade, stereo is still not possible on OS X even with new hardware?
Not at all. Currently shipping hardware http://www.apple.com/powermac
does stereo 3D in a window with currently shipping software
http://www.delsci.com/macpymol
Jan Kosinski wrote:
Is it possible to render a stereo view in pymol?
Jan Kosinski
Easily. Load the attached script and use it.
Andreas
--
--> Andreas Förster <--
8 rue Doudart de Lagrée, 38000 Grenoble
++33.(0)438.866201 and ++33.(0)456.452000
b5foan at skype and yahoo mess
Hi All:
just a quick follow up on Warren mentioning the Sharp 3D LCD display. After
a couple of trials with various drivers I got the LCD to work under the
following setup:
Nvidia Quadro FX1100 with driver V67.22
Windows XP with all the latest SPs and patches installed (may not matter)
One head o
Follow up to this. At least on one machine of the machines mentioned,
this script works fine when I copy/paste each line into idle. Strange
Charles Moad wrote:
The CVS version in linux seg faults when trying to launch this simple
stereo startup script. I get this on two very different li
Hi Joe
>> [cut - two projector stereo projetion system ]
> What kind of uses does your system see? Is it predominately
> used by researchers, or by classes, or a good mix between the two?
A very rough estimate
- 60% internal work, discussions with "wet" chemists, molecular
biologists and
On Mon, Nov 01, 2004 at 09:45:04PM +0100, EPF (Esben Peter Friis) wrote:
>
> We have great succes with PyMOL stereo on a two-projector system:
> - A Linux box with a Nvidia Quadro card provides the graphics (around
> $2000)
> - Two standard DLP projectors ($1500 each)
> - 2 Circular po
Hi Seth
First, I don't think it is possible at all to create shutter-glass
stereo on a standard DLP or LCD projector. I have actually tried this
(using an SGI) by going to very low refresh rates, such as 2x30 Hz. I
got some kind of effect, but the DLP/LCD projector does not sync
correctly to the r
Are you sure about the aspect ratio? If not just do ray and check the
resolution of the png. Then multiply the horisontal and vertical resolution
by a number and use the commands you mentioned. Or maybe it picks up only
one 2000, I have never actually tried that. Taller figures are usually
easi
Dirk,
stereo_angle is the amount of "toe-in"
stereo_shift is the horizontal displacement of the camera
Initially, stereo_angle=2.1 and stereo_shift=2.0
Generally, you don't need to adjust stereo_angle very much.
Stereo_shift is what you want to focus on. Try increasing it by 1 or 2.
For
You can also hold OPTION (Mac, ALT on PCs?) to duplicate an object when
you drag it. Thus, you can simply type the label once, click and drag
it with OPTION & SHIFT down and the label will be duplicated and locked
on axis during the move. I usually initiate the drag and then cross my
eyes for
Just to add a tip to this (should work in illustrator since it does in
photoshop). You can use your mouse (instead of the arrow keys), pressing
and holding down the shift key before clicking, to mouse the labels and
they will be locked to the axis you start your mouse motion with.
I have a photos
If you don't have a program such as Illustrator or Canvas, you can do the
same thing in powerpoint.
However, there is a small problem with exporting pictures from powerpoint,
but it can be overcome. I've pasted a description below.
__
This is absolutely the coolest tip for adding depth to labels in
raytraced stereopairs, it works great especially when implemented with
Warrens commands for creating the stereo pair
ray angle=-3
png image1.png
ray angle=3
png image2.png
Y
p.s. I am not having session save problems on 0.88 (fi
I followed your previous instructions but I am having problems seeing
stereo views. I see the blue line at the bottom of the screen, my
emitter's lcd briefly turns on then turns off when PyMol starts up, and
I can see a double image in the quadbuffer mode but I don't see the 3d
projection.
He
Tyler,
To get stereo on the Mac, you need the following:
(1) CRT monitor (LCD will not work)
(2) StereoGraphics blue-line HD15 pass-through adapter, hooked up to the
monitor cable you're using.
(3) StereoGraphics Emitter
(4) StereoGraphics Glasses (or NuVision glasses)
(5) PyMOL 0.88 installed fr
t] On Behalf Of Anthony
Duff
Sent: Tuesday, April 22, 2003 9:03 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Stereo pictures, light vector and shadows
I make stereo pictures by making two pictures, with the command "turn y,
6"
in between.
Now that I am looking into a
I make stereo pictures by making two pictures, with the command "turn y, 6"
in between.
Now that I am looking into a crevice, I have discovered a problem with this
simple method. When the view is rotated, the light vector moves with the
view. This results in the two pictures having differ
> From: Ricardo Aparicio [mailto:apari...@if.sc.usp.br]
> 1) what is the effect of command "stereo" in PyMol? Does it makes a
> confuse screen (like in O when one is not using stereo
> glasses)? If so,
> there is no sense in capture the image from the screen with
> png command.
No, it just fails
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