Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white
Hi Engin, the sequence viewer background and font colors are fixed in the latest open-source code (SVN rev 4041) and will be fixed in the next PyMOL release. Cheers, Thomas Engin Özkan wrote, On 09/04/13 19:59: Hi everybody, Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue numbers in the sequence if the background is set to white. I have been playing with all the seq_view_* settings (thanks for documenting them clearly within the Edit All Settings window!), especially seq_view_label_color, and this setting works if the background is not set to white. If the background is white (regardless of opaque background or not), many colors I tried display no font (or likely black font), *but* some colors do, and some colors display incorrect colors. RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and white for sequence numbers do not show. Grey, purple and brown look fine, but pink is a dimmed light blue, orange is green, and aquamarine is brown. After having too much fun with these colors, I thought I report this. Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version catches an error as it is starting, which may be related: libpng warning: iCCP: known incorrect sRGB profile Working on a Mac 10.6.8. Best, Engin -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/4140/ostg.clktrk ___ 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] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white
Hi, I experience the same with WinPyMOL 1.6.0.0 Incentive Build (running under Windows 7, NVidia Quadro 4000) - but not under Linux PyMOL 1.6.0.0. In addition I have the following related problem in WinPyMOL 1.6.0.0: when setting the background color (of the graphics window) to white, the background of the text console (switching with ESC key) remains black. In this case the text in this window is not visible at all (because it assumes it has white background and thus text color is inverted). When the background color is set to 'light grey' the text color becomes 'dark grey' (still on black background...). I have not experienced this problem in previous WinPyMOL Incentive Builds. Christoph Hi everybody, Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue numbers in the sequence if the background is set to white. I have been playing with all the seq_view_* settings (thanks for documenting them clearly within the Edit All Settings window!), especially seq_view_label_color, and this setting works if the background is not set to white. If the background is white (regardless of opaque background or not), many colors I tried display no font (or likely black font), *but* some colors do, and some colors display incorrect colors. RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and white for sequence numbers do not show. Grey, purple and brown look fine, but pink is a dimmed light blue, orange is green, and aquamarine is brown. After having too much fun with these colors, I thought I report this. Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version catches an error as it is starting, which may be related: libpng warning: iCCP: known incorrect sRGB profile Working on a Mac 10.6.8. Best, Engin -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk ___ 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 -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/4140/ostg.clktrk ___ 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] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white
Thanks, Vaheh. As I did say that in my first post, actually purple, brown, forest etc. work too. But none of the primary colors (RGB or CMYK) does. And a number of them (like pink) give wrong colors. And thanks for confirming the issue. Engin On 9/4/13 4:03 PM, Oganesyan, Vaheh wrote: Engin, If you go to Edit_all and change the seq_view_label_color to grey the numbers will become visible with white bkgr. Vaheh -Original Message- From: Engin Özkan [mailto:eoz...@stanford.edu] Sent: Wednesday, September 04, 2013 4:40 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white I forgot to explicitly say, this is only for the Sequence View panel, which has a black background regardless of the background parameter. And it applies to both sequence numbers and chain labels. Sequences themselves are displayed correctly. Engin On 9/4/13 12:59 PM, Engin Özkan wrote: Hi everybody, Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue numbers in the sequence if the background is set to white. I have been playing with all the seq_view_* settings (thanks for documenting them clearly within the Edit All Settings window!), especially seq_view_label_color, and this setting works if the background is not set to white. If the background is white (regardless of opaque background or not), many colors I tried display no font (or likely black font), *but* some colors do, and some colors display incorrect colors. RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and white for sequence numbers do not show. Grey, purple and brown look fine, but pink is a dimmed light blue, orange is green, and aquamarine is brown. After having too much fun with these colors, I thought I report this. Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version catches an error as it is starting, which may be related: libpng warning: iCCP: known incorrect sRGB profile Working on a Mac 10.6.8. Best, Engin -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.c lktrk ___ 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 -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/4140/ostg.clktrk ___ 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 To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/4140/ostg.clktrk ___ 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] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white
Engin, If you go to Edit_all and change the seq_view_label_color to grey the numbers will become visible with white bkgr. Vaheh -Original Message- From: Engin Özkan [mailto:eoz...@stanford.edu] Sent: Wednesday, September 04, 2013 4:40 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white I forgot to explicitly say, this is only for the Sequence View panel, which has a black background regardless of the background parameter. And it applies to both sequence numbers and chain labels. Sequences themselves are displayed correctly. Engin On 9/4/13 12:59 PM, Engin Özkan wrote: Hi everybody, Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue numbers in the sequence if the background is set to white. I have been playing with all the seq_view_* settings (thanks for documenting them clearly within the Edit All Settings window!), especially seq_view_label_color, and this setting works if the background is not set to white. If the background is white (regardless of opaque background or not), many colors I tried display no font (or likely black font), *but* some colors do, and some colors display incorrect colors. RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and white for sequence numbers do not show. Grey, purple and brown look fine, but pink is a dimmed light blue, orange is green, and aquamarine is brown. After having too much fun with these colors, I thought I report this. Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version catches an error as it is starting, which may be related: libpng warning: iCCP: known incorrect sRGB profile Working on a Mac 10.6.8. Best, Engin -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.c lktrk ___ 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 -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/4140/ostg.clktrk ___ 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 To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/4140/ostg.clktrk ___ 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] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white
I forgot to explicitly say, this is only for the Sequence View panel, which has a black background regardless of the background parameter. And it applies to both sequence numbers and chain labels. Sequences themselves are displayed correctly. Engin On 9/4/13 12:59 PM, Engin Özkan wrote: Hi everybody, Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue numbers in the sequence if the background is set to white. I have been playing with all the seq_view_* settings (thanks for documenting them clearly within the Edit All Settings window!), especially seq_view_label_color, and this setting works if the background is not set to white. If the background is white (regardless of opaque background or not), many colors I tried display no font (or likely black font), *but* some colors do, and some colors display incorrect colors. RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and white for sequence numbers do not show. Grey, purple and brown look fine, but pink is a dimmed light blue, orange is green, and aquamarine is brown. After having too much fun with these colors, I thought I report this. Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version catches an error as it is starting, which may be related: libpng warning: iCCP: known incorrect sRGB profile Working on a Mac 10.6.8. Best, Engin -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk ___ 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 -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/4140/ostg.clktrk ___ 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
