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
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
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
set antialias=1
ray 1200,1200
png file.png
and file.png
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 instructions
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 with 6629 driver).
OpenGL-based
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 programs are going to crash
too, not just VMD
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 7174 than they do on 6629.
Nuccyl:
As there was little
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 recently installed Pymol v0.97 on an SGI but the hardware stereo
mode
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, thanks. But, its not what I meant. I want to let 2 proteins
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 to generate an electrostatic potential map of the surface
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 thinking of buying
be 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 like to do
a short
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
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
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, directly
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=PowerMacmco=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 the
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
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
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
but it
, 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
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?
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=readlinesubmit=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
Hi all,
Anyone know if it's possible to use a RealD (Stereographics) E2SGI
emitter on Quadro hardware?
Thanks,
Sabuj Pattanayek
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
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
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
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
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On Wed, Feb 24, 2010 at 4:50 AM, Stefano Marzi ma...@igbmc.fr wrote:
Hi everybody,
Do you have any suggestion about new laptops that can support Active or
Passive Stereo 3D visualization with Pymol?
AS5738DG-6165
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
On Thu, Feb 25, 2010 at 7:12 AM, Christine Lee biobr...@gmail.com 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?
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
Try hex: http://www.loria.fr/~ritchied/hex/
On Fri, May 7, 2010 at 6:48 AM, Sona Vasudevan sona.vasude...@gmail.com 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
Hi,
On Sun, May 9, 2010 at 11:16 AM, Emiliano Ippoliti
e.ippol...@grs-sim.de 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
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?
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, smit...@atlas.cz wrote:
Hi all,
I would like to ask whether it is nvidia quadro 600 compatible with pymol 3d
stereo on windows 7? Do you
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.
bbat...@umich.edu wrote:
On Oct 5, 2012, at 4:33 PM, Sabuj Pattanayek sab...@gmail.com 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
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 :
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 GTX
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?
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