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
I thought all quadro cards supported stereo? (must admit that I'm not sure :-)
The 3 pin stereo connector is not needed to get stereo with the Asus monitors -
they get the stereo sync via DVI. But the stereo mode 10 and/or 11 must be
supported by the card and driver.
My main problem was to
and
still no stereo. However, when we upgraded from RHEL5 to RHEL6 everything
worked perfectly.
One point of difference between our setup and the one quoted below is we have
Stereo set to 10 and not 11. 11 is for VisionPro which uses RF instead of the
IR emitters.
Malcolm
From: EPF (Esben Peter
Hi Dick
A hint about your setup would be helpful :-) I Assume you use Linux.
Our ASUS VG278H monitors works fine in 3D stereo with Nvidia Quadro FX5800
cards. I have pasted my notes about how I configured X.
Cheers,
Esben
Asus VG278H flat panel 3D screens and Ubuntu 12.04
These screen
Hi PyMOLers
We recently bought Asus V278H monitors, which displays nice stereo under Linux
(Ubuntu 12.04). The monitors were bundled with Nvidia 3D vision v2 glasses. We
have Quadro FX5800 cards, but we do NOT use the 3-pin stereo port, but rather
the built-in emitter in the monitors. I have
Hi Dimitry
if you add an object=some name to your align command, then the sequences
are shown correctly aligned. The residues used in the alignment are shown in
their normal colors, the excluded onses are shown in gray, eg:
align obj01CA, obj02CA, object=alignment
I think you should
Hi Sabuj
Do these only work for programs under Linux that specifically
implement page flipping stereo?
Yes. The application must support OpenGL stereo. I have tested with the
following programs:
- VMD
- PyMOL
- Accelrys InsightII
- Accelrys DiscoveryStudio
The software that they
Hi David
Try http://www.edimensional.com/. They have a UK sales office.
We use those glasses with our Linux systems, and they work fine :-)
/Esben
Best Regards
Esben Peter Friis
Phone: +45 44461334
E-mail: e...@novozymes.com
Hi Michael
If the system is very big and causes the ray tracing to crash, try to
lower the hash_max setting. I think the default is 100. If the setting
is lower, it will be slower, but use less memory. (and vice versa :-)
All the best
Esben
-Original Message-
From:
Hi Chandra
If the sequences have some similarity, it is no problem :-)
align structure1 and chain B and name CA, structure2 and chain C and
name CA
All the best
Esben
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
Hi Rob
A bit confusing :-)
But the trick in such cases is usually to duplicate your object, and
show the cutaway surface on the original and the cartoon/helix/etc on
the copy.
The cutaway surface is often easier to create by box-selecting (with the
mouse) everything but the part that should
Hi Elo
The formula for cmputing the putty radius is found in layer1/ Extrude.c
in the source:
switch(source_field) {
default: /* b*/
scale = (range+(at-b - mean)/stdev)/range;
if(scale0.0F)
scale = 0.0F;
scale=(float)pow(scale,power);
Hi Elo
The formula for cmputing the putty radius is found in layer1/ Extrude.c
in the source:
switch(source_field) {
default: /* b*/
scale = (range+(at-b - mean)/stdev)/range;
if(scale0.0F)
scale = 0.0F;
scale=(float)pow(scale,power);
If the Mac version has the option hash_max, try to decrease it. The
rendering will take longer, but the memory usage will be lower. For
example:
set hash_max, 50
Try with different values. I think the default is 100.
Best wishes
Esben
-Original Message-
From:
Hi Blanton
You are probably looking for the symexp command. I don't remember the exact
syntax, but there is a small help text. You can also try to search the mail
archive.
Best wishes
Esben
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net on behalf of Blanton
Hi Arturas!
A - relatively - easy way to read DCDs into PyMOL is:
* Convert the .dcd to .trr using catdcd 4.0
(http://www.ks.uiuc.edu/Development/MDTools/catdcd/). At the same time you can
concatenate multiple .dcd files, remove solvent, skip frames, etc.
* Convert the .trr file to a
Hi Satya
You can use the command translate to move the individual objects in pymol. Is
takes a list of 3 floating points numbers as the translational vector.
I don't know how Pymol would handle 4000 objects, but an alternative might be
to load them as states within one object, and then use
Hi Stephen
I also use smooth surfaces - for visualizing results from small angle
xray scattering, which is a low resolution technique. I use:
set solvent_radius, 4
alter my_protein, vdw=4
sort
show surface, my_protein
Maybe you can set solvent_radius a little bit higher, but not much, as
,
Esben
-Original Message-
From: Warren DeLano [mailto:war...@delsci.com]
Sent: Mon 2005-10-17 22:06
To: EPF (Esben Peter Friis)
Subject: RE: [PyMOL] Geowall Testing
Esben,
Great!
Added: support for the internal gui, pop-up menus, sequence viewer, and
command line when using a passive
Message-
From: Warren DeLano [mailto:war...@delsci.com]
Sent: Mon 2005-10-17 22:43
To: EPF (Esben Peter Friis)
Subject: RE: [PyMOL] Geowall Testing
Esben,
If that is the case, then you don't actually have a Geowall -- you
have a professional stereo device setup that converts the active-stereo
Hi Yusuf
The OpenSource statistics software R (http://www.r-project.org) has many
packages that can do PCA, PLS and other multivariate analyses, which we have
used with great success.
There are several Pyhton interfaces to R, eg.
http://www.omegahat.org/RSPython/
http://rpy.sourceforge.net/
Hi Neil
Have you tried the command
set max_threads, 4
That should enforce 4 threads, even on single CPU machines. Then it's up
to the kernel scheduler to distribute them to the defferent CPUs
Cheers,
Esben
-Original Message-
From:
Is it possible to get graphics output higher than 72 dpi?
Yes:
- The OpenGL rendered graphics can only be saved in the resolution
displayed on the screen (using the png command)
- The raytracer can generate pictures of any size, eg.
ray 8000, 6000; png mypic.png
would generate the
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
Are you using the same platform for both Grasp and Pymol? I don't think
that big-endian maps (written by an SGI computer) can be read by a
little-endian platform, such as a x86 based PC.
- Esben
The problem is getting the phi map in grasp. Can somebody
explain me how to do it?
This is
I have mad a lot of these pictures, and the solution is to create two
objects for the substrate.
object1, displayed as sticks in the desired color, and
object2 dipslayed as spheres in the desired color(s)
and then set sphere_scale, 0.3, object2
Example (if the file contains a residue named
not sure these glasses
are available anymore.
Best regards
Esben
-Original Message-
From: Peter Haebel [mailto:peter.hae...@staff.uni-marburg.de]
Sent: 12. maj 2004 10:05
To: EPF (Esben Peter Friis)
Subject: Re: [PyMOL] Updated OpenGL Hardware Recommendations
Hi Esben
Hi Peter
Your posting is a few weeks old, but I could see no replies yet, so I'll try :-)
We have single-CPU Dell machines (3 GHz, 2GB RAM), but I suppose you just buy
CPU, disk and memory according to your needs (and money :-)
You don't write anything about OS, but according to your ps
Whops, sorry
You _do_ write it is Linux PCs ;-)
- Esben
Hi PyMOLers
I have a bunch of structures, for which I have calculated electrostatic
potential maps (using Gromacs and MEAD). I can easily load the
structures and corresponding maps into PyMOL and display a color coded
surface. But when I try to align the structures, only the atomic
coordinates
Hi Avram
This is possible in cartoon mode in the newer versions of PyMOL (i don't
remember exactly from which). You have to select highlight color in the
cartoon menu. The default color is grey, but can be changed by
set cartoon_highlight_color, color_name, object_name
Cheers,
Esben
To: EPF (Esben Peter Friis)
Sent: 14-09-03 20:28
Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL
Dear Esben,
no matter how hard I try, I cannot make pymol read a phi map converted
from avs with your utility. The .fld file was generated with the
potential program in the latest MEAD
-Original Message-
From: Warren L. DeLano
To: EPF (Esben Peter Friis)
Sent: 21-07-03 18:19
Subject: RE: [PyMOL] Nuvision stereo glasses?
Esben,
Are you sure you correctly configured the nVidia driver
(XF86Config) for Stereo? It's not automatic, but as AFAIK, all the FX's
are QBS capable
Hi PyMOL users,
MEAD's potential maps can be used in PyMOL, but it requires a little more
than a bit of tweaking, as the maps are in the AVS .fld format, which can
not be read by PyMOL. (These maps can be read by Dino, as Paulo just
mentioned). Also, PyMOL reads (as far as I can see) only
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