Re: [PyMOL] problems cloring sticks
Hi Jason, I tried to download the Pymol's last night version with the coloring sticks issue corrected. This was my first time facing the svn way of doing it, and I could not really manage to download it. Could you please help with this? thanks a lot in advanced Cheers, Ariel On Wed, 2011-06-08 at 13:34 -0500, Jason Vertrees wrote: For those using a more recent version of PyMOL (v1.4+) who have this stick coloring problem, can you please try: set use_shaders, 1 and let me know if that fixes the stick rendering issue? We've located the bug and are looking for a suitable workaround. (The colors are being set properly, but the video card isn't picking them up.) Cheers, -- Jason On Wed, Jun 1, 2011 at 12:04 PM, Ariel Talavera talav...@cim.sld.cumailto: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.cumailto: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.netmailto: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 [http://www.cim.co.cu/CIM.gif]www.cim.co.cu Disclaimer added by CodeTwo Exchange Rules 2007 www.codetwo.comhttp://www.codetwo.com -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev___ 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
Re: [PyMOL] problems cloring sticks
Hi, I'm also using Ubuntu 10.04 with a fresh installation of pymol 1.4.1 (Revision 3952) on a Intel GM965 graphics chip. Until now the coloring problem seems to be solved (even without 'set use_shaders, 1'). I'll keep on exploring all display features to check the new version, though ;) Before, I was using pymol 1.2r1 from the Ubuntu repository and I always had the coloring problem. So, thank you very much for solving it! Andreas Am 09.06.2011, 09:58 Uhr, schrieb Gianluigi Caltabiano chimic...@yahoo.it: With Ubuntu 10.04 LTS - Lucid Lynx and Pymol 1.4.1 it seems to solve the problem. thanks, Gianluigi Da: Jason Vertrees jason.vertr...@schrodinger.com A: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Inviato: Mer 8 giugno 2011, 20:34:46 Oggetto: Re: [PyMOL] problems cloring sticks For those using a more recent version of PyMOL (v1.4+) who have this stick coloring problem, can you please try: set use_shaders, 1 and let me know if that fixes the stick rendering issue? We've located the bug and are looking for a suitable workaround. (The colors are being set properly, but the video card isn't picking them up.) 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 -- 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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ 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
Re: [PyMOL] problems cloring sticks
Hi all, I pushed the change last night that fixes the stick coloring problem. You don't need the use_shaders setting either--it should just work. If, after properly upgrading PyMOL to last night's version, you still have issues with stick coloring, please let me know. Cheers, -- Jason On Thu, Jun 9, 2011 at 11:04 AM, Andreas Spitzmüller andreas.spitzmuel...@staff.uni-marburg.de wrote: Hi, I'm also using Ubuntu 10.04 with a fresh installation of pymol 1.4.1 (Revision 3952) on a Intel GM965 graphics chip. Until now the coloring problem seems to be solved (even without 'set use_shaders, 1'). I'll keep on exploring all display features to check the new version, though ;) Before, I was using pymol 1.2r1 from the Ubuntu repository and I always had the coloring problem. So, thank you very much for solving it! Andreas Am 09.06.2011, 09:58 Uhr, schrieb Gianluigi Caltabiano chimic...@yahoo.it: With Ubuntu 10.04 LTS - Lucid Lynx and Pymol 1.4.1 it seems to solve the problem. thanks, Gianluigi Da: Jason Vertrees jason.vertr...@schrodinger.com A: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Inviato: Mer 8 giugno 2011, 20:34:46 Oggetto: Re: [PyMOL] problems cloring sticks For those using a more recent version of PyMOL (v1.4+) who have this stick coloring problem, can you please try: set use_shaders, 1 and let me know if that fixes the stick rendering issue? We've located the bug and are looking for a suitable workaround. (The colors are being set properly, but the video card isn't picking them up.) 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 -- 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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ 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
Re: [PyMOL] problems cloring sticks
Hi Jason, How can I download Pymol's last night version? So far, the command line set use_shaders, 1 soleved the stick coloring problem for my pymol 1.4.1 on Ubuntu 11.04. Thanks a lot for your help. Cheers, ariel On Thu, 2011-06-09 at 10:16 -0500, Jason Vertrees wrote: PyMOL to last night's version 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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ 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
Re: [PyMOL] problems cloring sticks
Hi Ariel, If you're using a build from the Ubuntu team you'll need to wait for them to update PyMOL. If you're compiling from source, then you can just check out the code from SVN (https://sourceforge.net/scm/?type=svngroup_id=4546) and compile it. Cheers, -- Jason On Fri, Jun 10, 2011 at 1:11 AM, Ariel Talavera talav...@cim.sld.cu wrote: Hi Jason, How can I download Pymol's last night version? So far, the command line set use_shaders, 1 soleved the stick coloring problem for my pymol 1.4.1 on Ubuntu 11.04. Thanks a lot for your help. Cheers, ariel On Thu, 2011-06-09 at 10:16 -0500, Jason Vertrees wrote: PyMOL to last night's version 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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ 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
Re: [PyMOL] problems cloring sticks
Hi all, I'd just like to make it clear that we're not ignoring this problem. We have not fixed it because like the other Intel GM9x5 bugs, we cannot ever reproduce them on any machine we've tried--which is close to a dozen, now. We tried various machines and configurations, but still cannot get this to show the errors. When I get a machine that does reproduce these errors, we'll be able to make better headway. Last, some people have seen the problems go away after updating their drivers. Cheers, -- Jason On Sun, Jun 5, 2011 at 12:05 PM, David A. Horita dhor...@wfubmc.edu wrote: 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
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
Re: [PyMOL] problems cloring sticks
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
Re: [PyMOL] problems cloring sticks
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
Re: [PyMOL] problems cloring sticks
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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
