Yes, you can do nvidia 3d vision with this card under win 7 (not
linux!) with a 120Hz LCD monitor or a 120Hz DLP projector.
On Wed, Feb 8, 2012 at 2:03 AM, wrote:
> Hi all,
>
> I would like to ask whether it is nvidia quadro 600 compatible with pymol 3d
> stereo on windows 7? Do you have any exp
> 2) Is anyone out there succesfully running a 3D projektor using the DLP
> Link option (white flash in between images to sync the glasses). Is this
> technique being used at all (for true stereoscopic 3D software such as
> Pymol, Coot, Yasara, etc.) by anyone?
Yes, we have theInfocus IN3116 which
On Fri, Oct 5, 2012 at 3:48 PM, Bradford R. Battey, Jr.
wrote:
> On Oct 5, 2012, at 4:33 PM, Sabuj Pattanayek wrote:
>
>> We've tried the Asus VG278H with the built-in emitter and the nvidia
>> 3d vision v2 goggles (one pair included with the monitor) in Linux and
>&
You don't need a quadro with a 3 pin port to do stereo in linux
anymore, but you do need a "new" model quadro, e.g. a quadro 600. The
tradeoff is that you'll pay more for the 120hz monitors with the
built-in 3d vision v2 emitters, see here :
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-N
Even if this were true, the driver in linux won't allow 3d vision
(i.e. won't communicate with the emitter) unless it detects a quadro,
i.e. you'd need a driver hack.
On Thu, Dec 13, 2012 at 10:25 PM, Jeff Johns เจฟ จอห์น wrote:
> From
> http://stackoverflow.com/questions/8918945/how-to-do-stere
> It takes a bit of understanding. Am I correct that if the monitor does
> not have a built in emitter, the glasses need to be triggered from
> either a remote transmitter plugged into the 3 pin mini din port of a
> suitable quadro card for quad buffered, or to a USB port in the case of
> consumer
> Specifically, we'll have a demo version of PyMOL v1.6, PyMOL on the iPad,
> and even a sneak peek of Leap Motion (https://www.leapmotion.com/)
> controller integration with PyMOL.
Do you have it working under linux?
--
Hi,
This worked.
Thanks,
..Sabuj
Robert Campbell wrote:
prefixing a directory path. If you were like me and had:
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
in your pymol.com file, then it would not run that
cctbx_build/bin/python script. So you need to either change the abo
Doesn't shelx output map files in O (brix/dsn6) format?
from shelxpro:
[M] Map file for O from .fcf
If that doesn't work directly for pymol try using mapman to convert O to
whatever format you want.
Johanna Hakanpää wrote:
> Hi,
>
> Is there a way to read Shelx density maps to Pymol, directl
Do you have the URL?
D. Joe Anderson wrote:
> So, that sure looks like PyMOL to me (actually, four instances
> of it) running on the display of a PowerMac G5 on the
> newly-updated Apple Store website today.
>
> My question is, which structure is that?
>
nm, I found the url:
http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/72303/wo/iG1ZdpmENibK2kKdLwyNuAAR9NW/0.SLID?nclm=PowerMac&mco=586014F6
D. Joe Anderson wrote:
> So, that sure looks like PyMOL to me (actually, four instances
> of it) running on the display of a PowerMac G5 on t
Or you can dump to povray and render at whatever resolution you want,
but the image will not resemble exactly what is seen in the pymol viewer
window.
Peter Adrian Meyer wrote:
>>multiple structura alignment. I pointed out three structures for further
>>processing within all 12 structures. However
I don't know if it will make a difference (I don't even have a Mac) but
try opening it from a console using:
pymol -M
Serge Cohen wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Got exactly the same problem on a 800MHz TiBook
I was planning to try on a Dual G5, but had not the time toda
You can create an mrc map from a PDB using the pdb2mrc program in the
EMan package (http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/ and
http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/doc/progs/pdb2mrc.html).
Pdb2mrc allows you to specify parameters that would affect what a
theoretical cryo EM 3D reconstruct
try changing the name of the map to fofc.ccp4
load fofc.ccp4, fofc
isomesh fo1,fofc,3.0,(chain D),buffer=2.0,carve=2.8
S. Shanmuga Sundara Raj wrote:
> Hi,
>
> I tried to show the fofc map by using the following lines:
>
> load fofc.map, fofc
> isomesh fo1, fofc,3.0, (chain D), buffer=2.0
>
>
o upgrade your kernel. You can get
2.6.16 from kernel.org, copy your current .config into the root of the
source directory, run make oldconfig, hit enter a bunch of times, then
compile the kernel with make && make modules_install. You will have to
recompile the nvidia drivers for the new kernel too.
Hope that helps,
Sabuj Pattanayek
No consistent pattern. Both machines are x86, non-nvidia graphics cards
(which probably isn't helping). But, score at least one working setup
(yours) as a fully functional combination.
Yes always go with nvidia on linux x86/x86_64 if you can. Do you have an
ati/sis/3dlabs/intel product?
I use gentoo linux's portage to do all the compile work (emerge pymol).
From the ebuild it looks like you need these prerequisites:
python, pmw (python library), numeric (python library), tk, libpng,
zlib, and glut .
Praedor Atrebates wrote:
> Is anyone running pymol on an AMD64 system? If so,
This is using the binary distributions of APBS?
Becker, Joseph W wrote:
I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3
Professional. I've successfully installed maloc, but the apbs install
gives:
error: Failed dependencies
libreadline.so.4 is needed by apbs-0
I just installed the binary -i686 (not -i386), x86_64, and ia64 versions
of apbs and apbs tools for some redhat machines and tested them all
yesterday. None of the machines return anything when I do rpm -qa | grep
maloc . Do you actually need maloc if you're not compiling from source?
Becker,
I have these versions installed on i686 RH boxes:
readline-4.3-13
readline-devel-4.3-13
At
http://rpmfind.net/linux/rpm2html/search.php?query=readline&submit=Search+...
it shows that SuSE 9.3 uses readline-5.0-7.2.i586.rpm . I don't know if
that is going to be a problem. You may have to re-co
Hi all,
Anyone know if it's possible to use a RealD (Stereographics) E2SGI
emitter on Quadro hardware?
Thanks,
Sabuj Pattanayek
Making movies is really difficult in linux. I tried with xvidcap but
even if you set it to say 30fps or 25fps and use a small window size so
that the png/jpg file sizes aren't too big, it only still creates about
1 frame/sec. Which then if you try to render into a movie doesn't come
out properl
nyone noticed this problem or
know about a fix?
Thanks,
Sabuj Pattanayek
I've built the svn version and it no longer has this problem.
Sabuj Pattanayek wrote:
Hi,
We have a system running
cat /etc/redhat-release
Red Hat Enterprise Linux Client release 5 (Tikanga)
When we launch Open-Source PyMOL 0.99rc6, we can't type anything into
the Tcl/Tk dialogs
Hi,
What's the minimum recommend version of python against which pymol 1.0r0
should be run? I've seen that it doesn't work at all with 2.3 but does
with 2.4. Latest is 2.5.1.
Thanks,
Sabuj
EPF (Esben Peter Friis) wrote:
Hi David
Try http://www.edimensional.com/. They have a UK sales office.
Do these only work for programs under Linux that specifically implement
page flipping stereo? The software that they describe which must be
installed seems to be only for Windows (which als
Hi,
EPF (Esben Peter Friis) wrote:
Hi Sabuj
Do these only work for programs under Linux that specifically
implement page flipping stereo?
They deliver some drivers, which is for Windows only. On Linux, You must
use a stereo-enabled graphics card (ie. most Nvidia Quadro series, no
cheap GFor
Hi,
Warren DeLano wrote:
This has already been done with PyMOL. There's a video at:
http://molviz.cs.toronto.edu/molviz/
and the code is downloadable.
The stereo effect isn't so great with both eyes open, but I do think there is potential for use of head or object tracking as a means of c
eap as the Zalman
solution but will work with any other visualization apps out there
that have QBS support which don't support the Zalman.
HTH,
Sabuj Pattanayek
--
This SF.Net email is sponsored by the Verizon Deve
On Wed, Feb 24, 2010 at 4:50 AM, Stefano Marzi wrote:
> Hi everybody,
>
> Do you have any suggestion about new laptops that can support Active or
> Passive Stereo 3D visualization with Pymol?
AS5738DG-6165
http://us.acer.com/acer/productv.do?LanguageISOCtxParam=en&kcond61e.c2att101=56746&sp=page
> Graphics Card is a nVidiaGEFORCE QUADRO FX 1800.
See the Active Stereo 3D (High-Refresh) Displays section on this pymol
wiki page:
http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#Active_Stereo_3D
> PyMOL official recommendations was the Zalman ZMM220W, but this is not
I don't thi
On Thu, Feb 25, 2010 at 7:12 AM, Christine Lee wrote:
> Dear,
>
> Based on my personal experience, I do not recommend Acer, It is really
> poor hardware. Or give it a try and after some time you will realize
> how poor it is.
Yeah, I agree. But anyone know of any other 3D laptops? There are
thes
> I just tried exactly the same thing with OpenSuSE 11.2 and couldn't get it
> to work at all. The reason, at least how I got it after a long, long
> discussion with custhelp.nvidia appears to be that some distributions mount
> USB devices under /proc/bus/usb/devices (works...) and some under
> /de
Try hex: http://www.loria.fr/~ritchied/hex/
On Fri, May 7, 2010 at 6:48 AM, Sona Vasudevan wrote:
> Hello All,
>
> I would greatly appreciate if anyone can suggest a PC based docking program
> for teaching purposes? I am trying ArgusLab, but that seems too unstable.
>
> Thanks much!
>
> Sona
> -
Hi,
On Sun, May 9, 2010 at 11:16 AM, Emiliano Ippoliti
wrote:
> Dear Users,
>
> in my University I have an hardware system formed by:
>
> 1 - PC with Nvidia Quadro FX 4800 graphics card.
> 2 - 64-bit Operating system Windows 7 Professional
> 3 - Projector ACER H5360 DLP 720P (3D ready) connected
> First, the PyMOL website has been completely changed. I wanted it to
> be on par with the quality of images and movies one can make in PyMOL.
> I also wanted to make sure it didn't look too stodgy corporate-like.
> Anyhow, it's up and I like it alot, actually.
I see "USER-SPONSORED" and "OPEN-
heh, nm I found it :
Open-Source and Educational Users: Please consult & participate in the
PyMOL Community Wiki instead, which has tons of FREE usage
information. The Official PyMOL Downloads and Documentation site is
for PyMOL Sponsors only.
On Thu, Aug 19, 2010 at 2:48 PM, Sabuj Pattan
> We've had great success with the ViewSonic PJD6531w
> (http://www.viewsonic.com/products/pjd6531w.htm). It's bright, clear
So are you guys using the DLP link (3d sync) technology of the
projector with DLP link capable glasses?
---
..so is there anyway to load two phi maps and map them to the surfaces
of their correlating molecules without exceeeding their respective
surface boundaries?
Thanks,
Sabuj Pattanayek
so it looks
like one system.
Thank you very much,
Sabuj Pattanayek
Michael George Lerner wrote:
Hi,
I've been meaning to update APBS tools so that some of the warnings are
larger and better explained.
WARNING: 53 atoms did not have properties assigned
means that PyMOL couldn'
n flickers like its in stereo mode. Is there some
kind of pymol startup switch or environment variable to disable loading
into a stereo window?
Michael George Lerner wrote:
Hi,
On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:
Dear Mr. Lerner,
Thanks for letting me know about the PDB2PQR server.
I have been trying to install pymol in red hat linux 8.0 using the
redhat rpm package for this version. I am getting an error saying
"error: Failed dependencies:
tkinter >= 2.0.0 is needed by pymol-0.97-1.rh80.py22"
How do I get tkinter 2.0.0?
http://rpmfind.net is available for all your rpm n
got this to work once
with a different pse file, tried restarting pymol but I can't get it to
work anymore. I'm using 0_98beta27 on linux.
Thanks,
Sabuj Pattanayek
in
the display window I see it as gray ..strange.
Sorry if this is really confusing, but I hope it's some error in the pml
and not in pymol.
Thanks,
Sabuj Pattanayek
Matt Franklin wrote:
Sabuj Pattanayek wrote:
Hi,
I set smooth lines from the menu, then I did:
set orthoscopic=1
s
electrostatics overview), and well i can't get the delphi source to
recompile for larger sets of atoms on linux using g77.
I hope this helps and that the apbs server works for you.
..Sabuj Pattanayek
fredb wrote:
Hi Everyone,
When I try to use PyMol and APBS (according to the instructio
ring works very
nicely in vmd 1.8.3.
Sorry for posting this on both mailing lists, just trying to avoid
reposting.
..Sabuj Pattanayek
HuiZhe Li wrote:
just upgraded nvidia driver from 6629 to 7167 (Linux,
RHEL 4) and pymol crashes when a molecule is load. is
there a fix? (pymol worked fine wit
oops:
"I have a GeForce 5500 FX on another machine and it doesn't have these
programs" should be "I have a GeForce 5500 FX on another machine and it
doesn't have these *problems*".
Sabuj Pattanayek wrote:
Yeah I have the same problem in the beta pymol, hav
th the
contents of your email.
..Sabuj Pattanayek
John Stone wrote:
Sabuj,
That's really interesting. It sounds to me like NVidia's new driver
has some sort of problem with drawing quads or quad strips in immediate mode.
If that's what's going on, then a lot of other progra
ashes with certain representation that I outlined in a
previous email to vmd-l.
Thanks,
Sabuj Pattanayek
tree wrote:
> NVidia:
> I just got the 7174 driver (for 64-bit Linux). PyMol works fine, no
> crashes. What do other folks see with 7174? My openGL apps run
> nominally faster on 71
Stereo in
pymol-0_98beta27-bin-irix65-r10k the screen resolution automatically
changes to 1024x768_96s from 1280x1024_30f (I wish it would switch back
when i turn off hardware stereo, but it does not).
Hope that helps,
Sabuj Pattanayek
Ambert Nicolas wrote:
> Hello PYMOLers,
>
>I've
atching matrices to
choose from, and will even show you the sequence alignment if you want.
You can even interesting residues in the sequence alignment window and
it will select them in realtime in the structure viewing window.
Hope that helps,
Sabuj Pattanayek
yunbo.song wrote:
> Ok, t
without having to compile anything, to look into GRASP2 for windows. It
is at http://trantor.bioc.columbia.edu/grasp2/ . You can import the .phi
maps from grasp into many applications including pymol and visualize
them also.
Hope that helps,
Sabuj Pattanayek
migalepa wrote:
> I've been trying
m for graphics so you should have no problems. In general
a dedicated ati or nvidia chip has more opengl capabilities than
embedded intel or sis graphics chips. A $50 upgrade to 512MB would help
tremendously however.
Hope that helps,
Sabuj Pattanayek
Luca Fenu wrote:
> Hi everyone,
>
> I'm
good for conferences, and would be geeky cool also.
thanks in advance,
Sabuj Pattanayek
Andreas Henschel wrote:
> Hi there,
>
> Is it possible to display both a png file (using load_png) AND
> some molecule at the same time?
> It sure sounds geeky, but the rationale is that I would
It looks like a CGO (compiled graphics object) behind the molecule, then
rendered using pov-ray, probably a script floating around to do this
somewhere on the internets.
Corinne Zeitler wrote:
Hi,
I was wondering if anyone knows how to produce the type of image in
Pymol that is on the Pymol
I use a cheap microsoft optical (or basic optical) usb mouse on linux,
so it should work on your macosx.
If you want something more configurable under macosx and don't want to
destroy the "Appleness" of your computer with an MS mouse then this
might work for you http://www.apple.com/mightymous
Actually I was wondering the same thing, except how to set it up in
linux. I was able to compile the cctbx but I'm not sure how to get it to
show up as a python module so that Pymol scripts (e.g. Dr. Campbell's
draw_cell.py) can work. Any help would be greatly appreciated.
Yi Zhang wrote:
Dea
ssibly be that when pymol is
executed it loads a new environment and thus the cctbx paths are not set
in this new environment?
Thanks,
Sabuj Pattanayek
Robert Campbell wrote:
Hi,
* Sabuj Pattanayek [2005-08-18 16:08] wrote:
Actually I was wondering the same thing, except how to set it up i
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