Re: [PyMOL] hardware stereo using pymol
On Saturday 17 January 2004 03:25, Dr. S. Frank Yan wrote: > I'm using stereographics crystaleye with e-2 emitter > and Quadro2 Pro graphics card, which does support the > emitter. I am able to set the stereo on, and the > screen starts to flick a little; however, the emitter > is not turned on by the program and therefore no > stereo. Stereographics claims that the emitter has to > be turned on/off by application program when the > stereo is enabled/disabled. I was wondering if anyone > has experience with that. Thanks a lot, Frank Which OS is that? If you are on Linux, make sure you configure your X11 properly: 1) use the "nvidia" driver 2) load the "glx" module 3) remove the "dri" and "GLcore" modules 4) Most important: add Option "Stereo" "3" to the nvidia device section to turn on support for onboard stereo Regards Andreas -- Andreas Aemissegger, Laboratory of Organic Chemistry ETH Hoenggerberg - HCI F322, 8093 Zurich, Switzerland Phone: +41 1 632 2972, Fax: +41 1 632 1486 Mail: aemisseg...@org.chem.ethz.ch, WWW: http://www.protein.ethz.ch PGP key on request
Re: [PyMOL] homologous alignments?
Hello, I am unable to read the archive at the moment so can anyone tell me the command that allows colouring of the edge of helices and strands (usually grey). I think this was posted recently but I don't have it in any of my saved scripts. Many thanks, Camille Dr Camille Shammas Medical Research Council Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK. Tel: +44 (0)1223 402407 Mobile: 07812035842 E-mail: cami...@mrc-lmb.cam.ac.uk
RE: [PyMOL] homologous alignments?
Camille, If I understand your question, you're looking for the setting which creates a discrete color transition at the edges of helices and strands, instead of blending. It is: set cartoon_discrete_colors, on For example color grey, name ca color yellow, ss s and name ca color red, ss h and name ca set cartoon_discrete_colors, on Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of cami...@mrc-lmb.cam.ac.uk > Sent: Monday, January 19, 2004 7:37 AM > To: Warren L. DeLano > Cc: 'Michael Bovee'; pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] homologous alignments? > > Hello, >I am unable to read the archive at the moment so can anyone tell > me the command that allows colouring of the edge of helices and strands > (usually grey). I think this was posted recently but I don't have it in > any of my saved scripts. > > Many thanks, > Camille > > Dr Camille Shammas > Medical Research Council Laboratory of Molecular Biology Hills Road, > Cambridge CB2 2QH, UK. > Tel: +44 (0)1223 402407 > Mobile: 07812035842 > E-mail: cami...@mrc-lmb.cam.ac.uk > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration See the > breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] working directory
Lesley,
If you always want PyMOL to start in a different directory, you
can create a ".pymolrc" file in you home directory with a command like
cd /users/lesley/scripts
Which will be executed every time you start PyMOL.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Lesley Debono
> Sent: Sunday, January 18, 2004 11:56 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] working directory
>
> i have pymol installed on an OSX machine. When I begin pymol i am in
> the root ("\") directory. My scripts are in a different directory. Is
> there a way I can begin in another directory when starting Pymol?
>
> cheers
> Lesley
>
>
>
> ---
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] hardware stereo using pymol
Hi, Thanks for the reply. We set them; however, it is still not working yet. I can see the pymol screen is flickering, but the emitter is apparently not turned on (no red light). --- Andreas Aemissegger wrote: > On Saturday 17 January 2004 03:25, Dr. S. Frank Yan > wrote: > > I'm using stereographics crystaleye with e-2 > emitter > > and Quadro2 Pro graphics card, which does support > the > > emitter. I am able to set the stereo on, and the > > screen starts to flick a little; however, the > emitter > > is not turned on by the program and therefore no > > stereo. Stereographics claims that the emitter > has to > > be turned on/off by application program when the > > stereo is enabled/disabled. I was wondering if > anyone > > has experience with that. Thanks a lot, Frank > > Which OS is that? If you are on Linux, make sure you > configure your X11 > properly: > 1) use the "nvidia" driver > 2) load the "glx" module > 3) remove the "dri" and "GLcore" modules > 4) Most important: add > Option "Stereo" "3" > to the nvidia device section to turn on support for > onboard stereo > > > Regards > > Andreas > -- > Andreas Aemissegger, Laboratory of Organic Chemistry > ETH Hoenggerberg - HCI F322, 8093 Zurich, > Switzerland > Phone: +41 1 632 2972, Fax: +41 1 632 1486 > Mail: aemisseg...@org.chem.ethz.ch, WWW: > http://www.protein.ethz.ch > PGP key on request > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and > Integration > See the breadth of Eclipse activity. February 3-5 in > Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users __ Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes http://hotjobs.sweepstakes.yahoo.com/signingbonus
