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 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
[PyMOL] Newline character in labels
Hi, I'd like to label a couple of CA atoms in with their AA code, residue number and b-factor. Since this gets a long label, I want to split it to get two lines. For example, if I have the CA atom of Asn124 with a b-factor of 36.2, I want it to be labelled as follows: Asn124 36.2 However, I cannot get the line break into the label! Is there any possibility? I tried things like \n or unicode encoding u\u000a in combination with a unicode font (label_font_id 15). But I couldn't manage to get the label on two lines. Thanks for any hints! Andreas PS: Please excuse if this message is posted twice, but it seems to me that my first attempt didn't come through to you. (This is my first posting on this list.) -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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
