Ariel, I would just add to Andreas' reply that in my case (onboard intel GMA-HD, Suse linux, core i3) either using ray (and if you have a lot of memory, set setting->rendering->memory-> use most) or saving the pse and making images on a windows PC (or a linux PC with an nvidia graphics card) are the workarounds I use. Not a solution per se, but this seems to be an issue between OpenGL and Intel (although I've only seen problems with Pymol, and not vmd).
-David David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston Salem, NC 27157, USA ________________________________________ From: Andreas Spitzmüller [andreas.spitzmuel...@staff.uni-marburg.de] Sent: Sunday, June 05, 2011 11:09 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] problems cloring sticks Hi Ariel, I'm facing the same problem on my Ubuntu laptop with an onboard Intel graphics chip. And as far as I know it is a problem of the linux graphics driver. >> From my side this is a huge problem for making figures. However, I found that ray tracing is not affected by this bug. I know that this is for sure not convenient, but still it is possible to make figures for publication or presentation slides. Just try the 'ray' command to see if this yields correct coloring for you, too. Regards, Andreas Am 05.06.2011, 08:29 Uhr, schrieb Ariel Talavera <talav...@cim.sld.cu>: > Hi Jason, > > After some struggle, I finally compiled the last open source version, > Pymol 1.4.1. Unfortunately, the same problem persist. I still not able > to properly colored residues shown as sticks. > >> From my side this is a huge problem for making figures. > > Best regards, > Ariel > > > On Wed, 2011-06-01 at 12:35 -0500, Jason Vertrees wrote: >> Hi Ariel, >> >> This is a known problem on some machines with ATI or Intel video >> cards. You can try upgrading to a newer version of PyMOL. Also, >> please check that your video driver is the newest for your video card. >> If I find a solution on our side that fixes this, I'll update the >> open-source. >> >> Cheers, >> >> -- Jason >> >> On Wed, Jun 1, 2011 at 12:04 PM, Ariel Talavera <talav...@cim.sld.cu> >> wrote: >> > Hi Pymolers, >> > >> > I am having problems coloring residues when they are shown as stick. >> The >> > coloring is properly working for the other representations like, >> lines, >> > surface or spheres. I am using Pymol 1.2r2 under Ubuntu 11,04. >> > >> > Thanks in advanced, >> > best regrads, >> > Ariel >> > >> > >> ------------------------------------------------------------------------ >> > Centro de Inmunologia Molecular >> > phone: +537 2717933 >> > e-mail: c...@cim.sld.cu >> > web: www.cim.co.cu >> > >> ------------------------------------------------------------------------ >> > >> > >> > Disclaimer added by CodeTwo Exchange Rules 2007 >> > http://www.codetwo.com >> > >> > >> > >> ------------------------------------------------------------------------------ >> > Simplify data backup and recovery for your virtual environment with >> vRanger. >> > Installation's a snap, and flexible recovery options mean your data >> is safe, >> > secure and there when you need it. Data protection magic? >> > Nope - It's vRanger. Get your free trial download today. >> > http://p.sf.net/sfu/quest-sfdev2dev >> > _______________________________________________ >> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: >> http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > >> >> >> > > > ------------------------------------------------------------------------ > Centro de Inmunologia Molecular > phone: +537 2717933 > e-mail: c...@cim.sld.cu > web: www.cim.co.cu > ------------------------------------------------------------------------ > > > Disclaimer added by CodeTwo Exchange Rules 2007 > http://www.codetwo.com > > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with > vRanger. > Installation's a snap, and flexible recovery options mean your data is > safe, > secure and there when you need it. Discover what all the cheering's > about. > Get your free trial download today. > http://p.sf.net/sfu/quest-dev2dev2 > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Andreas Spitzmüller, M.Sc (Bioinformatics) Group Prof. Gerhard Klebe Institute of Pharmaceutical Chemistry Philipps-Universität Marburg Marbacher Weg 6 D-35037 Marburg Phone: +49-6421-28-21339 Email: andreas.spitzmuel...@staff.uni-marburg.de www.agklebe.de ------------------------------------------------------------------------------ Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Discover what all the cheering's about. Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Discover what all the cheering's about. Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
