[PyMOL] Quadro4 + newest nvidia drivers => broken stereo

[Esben J. B. <esb...@ro...>]

Hi All=0A    A quick fix to the problem with the newest nVIDIA linux driver=
s and broken stereo is to install the nvidia-glx-legacy package if it is av=
ailable for your distribution. In Ubuntu this contains the 7184 driver whic=
h was the last to support  TNT, TNT2, TNT Ultra, GeForce, and GeForce2 chip=
sets. However, it also supports quadro 4 chipsets with working stereo, even=
 though the package description doesnt mention this.=0A    sudo apt-get ins=
tall 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.=0A=0AAnother note: the new composite extension br=
eaks stereo support. =0Asudo nvidia-xconfig --no-composite fixes this on Ed=
gy Eft.=0A=0AEsben=0A=0A=0A----- Original Message ----=0AFrom: "pymol-users=
-re...@li..." <pym...@li...>=
=0ATo: pym...@li...=0ASent: Thursday, October 26, 2006=
 9:28:22 PM=0ASubject: PyMOL-users Digest, Vol 5, Issue 21=0A=0ASend PyMOL-=
users mailing list submissions to=0A    pym...@li...=
=0A=0ATo subscribe or unsubscribe via the World Wide Web, visit=0A    https=
://lists.sourceforge.net/lists/listinfo/pymol-users=0Aor, via email, send a=
 message with subject or body 'help' to=0A    pym...@li...u=
rceforge.net=0A=0AYou can reach the person managing the list at=0A    pymol=
-us...@li...=0A=0AWhen replying, please edit your Sub=
ject line so it is more specific=0Athan "Re: Contents of PyMOL-users digest=
..."=0A=0A=0AToday's Topics:=0A=0A   1. Transparent cartoon disapearing wit=
h ray trace=0A      (Emeric Wasielewski)=0A   2. more color in pymol (shive=
sh kumar)=0A   3. Re: Transparent cartoon disapearing with ray trace=0A    =
  (Mat...@im...)=0A=0A=0A----------------------------------=
------------------------------------=0A=0AMessage: 1=0ADate: Wed, 25 Oct 20=
06 19:11:27 -0500=0AFrom: Emeric Wasielewski <Was...@ma...>=
=0ASubject: [PyMOL] Transparent cartoon disapearing with ray trace=0ATo: py=
mol...@li...=0AMessage-ID: <453...@ma...>=
=0AContent-Type: text/plain; charset=3DISO-8859-1; format=3Dflowed=0A=0AHel=
lo everybody,=0A=0AI wish to represent the backbone of my protein in cartoo=
n with a =0Atransparency of 0.6. Around it I show the surface with a transp=
arency of =0A0.4. (the aim is to highlight some specific residues by showin=
g their =0Aside chains in stick without transparency).=0AI can see the want=
ed result in OpenGL view. But when I raytrace the =0Apicture a kind of "Cop=
perfield" effect happens: the cartoon backbone =0Adisappears (NB: it happen=
s for any kind of combination of transparency =0Avalue for cartoon and surf=
ace).=0AIs anybody have an idea of what is happening ?=0A=0AThanks,=0A=0AEm=
eric=0A-- =0A+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=
=3D+=3D+=3D+=3D+=3D+=0AEmeric Wasielewski, Ph. D.=0ADepartment of Biochemis=
try and Molecular Biology=0A=0AMayo Clinic College of Medicine=0AGuggenheim=
 15-93=0A200, First Street SW=0ARochester, MN 55905, USA=0A=0AOffice: (507)=
 284 9189 Fax: (507) 284 1209=0Amailto: eme...@ma...=0A=0A=
=0A=0A------------------------------=0A=0AMessage: 2=0ADate: Wed, 25 Oct 20=
06 21:59:06 -0700 (PDT)=0AFrom: shivesh kumar <shi...@ya...>=0ASub=
ject: [PyMOL] more color in pymol=0ATo: pym...@li...=
=0AMessage-ID: <200...@we...>=0AConte=
nt-Type: text/plain; charset=3Diso-8859-1=0A=0ADear all,=0AHow can I use th=
e color option in the Setting=0Amenu(Edit all) to get more color in the car=
toon.Thanx.=0AShivesh=0A=0Ashivesh=0A=0A___________________________________=
_______________=0ADo You Yahoo!?=0ATired of spam?  Yahoo! Mail has the best=
 spam protection around =0Ahttp://mail.yahoo.com =0A=0A=0A=0A--------------=
----------------=0A=0AMessage: 3=0ADate: Thu, 26 Oct 2006 10:26:47 -0400=0A=
From: Mat...@im...=0ASubject: Re: [PyMOL] Transparent carto=
on disapearing with ray trace=0ATo: Emeric Wasielewski <Wasielewski.Emeric@=
mayo.edu>=0ACc: pym...@li...=0AMessage-ID:=0A    <OFDF=
434...@im...>=0A    =
=0AContent-Type: text/plain; charset=3DUS-ASCII=0A=0A=0A=0Apymol-users-boun=
ce...@li... wrote on 10/25/2006 08:11:27 PM:=0A=0A> Hello eve=
rybody,=0A>=0A> I wish to represent the backbone of my protein in cartoon w=
ith a=0A> transparency of 0.6. Around it I show the surface with a transpar=
ency of=0A> 0.4. (the aim is to highlight some specific residues by showing=
 their=0A> side chains in stick without transparency).=0A> I can see the wa=
nted result in OpenGL view. But when I raytrace the=0A> picture a kind of "=
Copperfield" effect happens: the cartoon backbone=0A> disappears (NB: it ha=
ppens for any kind of combination of transparency=0A> value for cartoon and=
 surface).=0A> Is anybody have an idea of what is happening ?=0A>=0A> Thank=
s,=0A>=0A> Emeric=0A=0AHi Emeric -=0A=0APymol has a few different ways of h=
andling multiple nested transparent=0Asurfaces.  The default is to just sho=
w the one closest to the viewer=0A(uni-layer transparency).  This gives pre=
ttier pictures with a single=0Asurface, since you don't see the backside of=
 the protein or any pockets in=0Athe surface.  However, for your purposes, =
you want multi-layer=0Atransparency.  To select this, choose "Setting->Tran=
sparency->Multi-layer".=0A=0AI just confirmed that this works.  I find the =
results a bit busy, unless=0Ayou're looking at just a small part of the pro=
tein.  You may need to hide=0Abackground details with the clipping planes.=
=0A=0A- Matt=0A=0A=0A--=0AMatthew Franklin , Ph.D.=0ASenior Scientist, ImCl=
one Systems=0A180 Varick Street, 6th floor=0ANew York, NY 10014=0Aphone:(91=
7)606-4116   fax:(212)645-2054=0A=0A=0AConfidentiality Note:  This e-mail, =
and any attachment to it, contains=0Aprivileged and confidential informatio=
n intended only for the use of the=0Aindividual(s) or entity named on the e=
-mail.  If the reader of this e-mail=0Ais not the intended recipient, or th=
e employee or agent responsible for=0Adelivering it to the intended recipie=
nt, you are hereby notified that=0Areading it is strictly prohibited.  If y=
ou have received this e-mail in=0Aerror, please immediately return it to th=
e sender and delete it from your=0Asystem.  Thank you.=0A=0A=0A=0A=0A------=
------------------------=0A=0A---------------------------------------------=
----------------------------=0AUsing Tomcat but need to do more? Need to su=
pport web services, security?=0AGet stuff done quickly with pre-integrated =
technology to make your job easier=0ADownload IBM WebSphere Application Ser=
ver v.1.0.1 based on Apache Geronimo=0Ahttp://sel.as-us.falkag.net/sel?cmd=
=3Dlnk&kid=3D120709&bid=3D263057&dat=3D121642=0A=0A------------------------=
------=0A=0A_______________________________________________=0APyMOL-users m=
ailing list=0AP...@li...=0Ahttps://lists.sourceforge=
.net/lists/listinfo/pymol-users=0A=0A=0AEnd of PyMOL-users Digest, Vol 5, I=
ssue 21=0A******************************************=0A=0A=0A=0A=0A