Hi All
A quick fix to the problem with the newest nVIDIA linux drivers and broken
stereo is to install the nvidia-glx-legacy package if it is available for your
distribution. In Ubuntu this contains the 7184 driver which was the last to
support TNT, TNT2, TNT Ultra, GeForce, and GeForce2 chipsets. However, it also
supports quadro 4 chipsets with working stereo, even though the package
description doesnt mention this.
sudo apt-get install nvidia-glx-legacy, close X, rmmod nvidia or restart,
restart X. There might be a problem with the initrd image containing the wrong
kernel-driver, so that rmmod nvidia have to be issued after the kernel have
mounted root and before X is started.
Another note: the new composite extension breaks stereo support.
sudo nvidia-xconfig --no-composite fixes this on Edgy Eft.
Esben
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Today's Topics:
1. Transparent cartoon disapearing with ray trace
(Emeric Wasielewski)
2. more color in pymol (shivesh kumar)
3. Re: Transparent cartoon disapearing with ray trace
(matthew.frank...@imclone.com)
----------------------------------------------------------------------
Message: 1
Date: Wed, 25 Oct 2006 19:11:27 -0500
From: Emeric Wasielewski <wasielewski.eme...@mayo.edu>
Subject: [PyMOL] Transparent cartoon disapearing with ray trace
To: pymol-users@lists.sourceforge.net
Message-ID: <453ffd2f.7080...@mayo.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hello everybody,
I wish to represent the backbone of my protein in cartoon with a
transparency of 0.6. Around it I show the surface with a transparency of
0.4. (the aim is to highlight some specific residues by showing their
side chains in stick without transparency).
I can see the wanted result in OpenGL view. But when I raytrace the
picture a kind of "Copperfield" effect happens: the cartoon backbone
disappears (NB: it happens for any kind of combination of transparency
value for cartoon and surface).
Is anybody have an idea of what is happening ?
Thanks,
Emeric
--
+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+
Emeric Wasielewski, Ph. D.
Department of Biochemistry and Molecular Biology
Mayo Clinic College of Medicine
Guggenheim 15-93
200, First Street SW
Rochester, MN 55905, USA
Office: (507) 284 9189 Fax: (507) 284 1209
mailto: emeric.wasielew...@mayo.edu
------------------------------
Message: 2
Date: Wed, 25 Oct 2006 21:59:06 -0700 (PDT)
From: shivesh kumar <shivesh_...@yahoo.com>
Subject: [PyMOL] more color in pymol
To: pymol-users@lists.sourceforge.net
Message-ID: <20061026045906.11429.qm...@web53604.mail.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Dear all,
How can I use the color option in the Setting
menu(Edit all) to get more color in the cartoon.Thanx.
Shivesh
shivesh
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------------------------------
Message: 3
Date: Thu, 26 Oct 2006 10:26:47 -0400
From: matthew.frank...@imclone.com
Subject: Re: [PyMOL] Transparent cartoon disapearing with ray trace
To: Emeric Wasielewski <wasielewski.eme...@mayo.edu>
Cc: pymol-users@lists.sourceforge.net
Message-ID:
<ofdf43457f.417213dc-on85257213.004e337a-85257213.004f5...@imclone.com>
Content-Type: text/plain; charset=US-ASCII
pymol-users-boun...@lists.sourceforge.net wrote on 10/25/2006 08:11:27 PM:
> Hello everybody,
>
> I wish to represent the backbone of my protein in cartoon with a
> transparency of 0.6. Around it I show the surface with a transparency of
> 0.4. (the aim is to highlight some specific residues by showing their
> side chains in stick without transparency).
> I can see the wanted result in OpenGL view. But when I raytrace the
> picture a kind of "Copperfield" effect happens: the cartoon backbone
> disappears (NB: it happens for any kind of combination of transparency
> value for cartoon and surface).
> Is anybody have an idea of what is happening ?
>
> Thanks,
>
> Emeric
Hi Emeric -
Pymol has a few different ways of handling multiple nested transparent
surfaces. The default is to just show the one closest to the viewer
(uni-layer transparency). This gives prettier pictures with a single
surface, since you don't see the backside of the protein or any pockets in
the surface. However, for your purposes, you want multi-layer
transparency. To select this, choose "Setting->Transparency->Multi-layer".
I just confirmed that this works. I find the results a bit busy, unless
you're looking at just a small part of the protein. You may need to hide
background details with the clipping planes.
- Matt
--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116 fax:(212)645-2054
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