Re: [PyMOL] Select different set of atoms in different molecules
What about the following commands: select mystuff, resi 1-3 and m1 select otherstuff, resi 7-9 and m2 Cheers, ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 9/5/2013 3:40 PM, Alessia Visconti wrote: Dear pyMOL users, I'm puzzled about how to solve an apparently simple task. I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select two different sets of atoms from each of them. Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] from m2. I tried several combinations of "load" and "select", but no option worked. The last selection is always applied to both molecules. I also Googled it, without any success. Does anyone know if its possible to make a selection in isolation over a given molecule? Any suggestion will be highly appreciated! Thanks in advance, Alessia -- 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=58041391&iu=/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=58041391&iu=/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] Select different set of atoms in different molecules
Hi Allesia, I am not quite sure how to want to select the atoms, but if you want to have the selected atoms of both m1 and m2 in the same selection (here s1), then try this: select s1, (m1 and id 1-3) or (m2 and id 7-9) if you want two different selections, just do select s1, m1 and id 1-3 select s2, m2 and id 7-9 Hope that helps, Bernhard On Sep 5, 2013, at 12:40 PM, Alessia Visconti wrote: > Dear pyMOL users, > I'm puzzled about how to solve an apparently simple task. > > I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select two > different sets of atoms from each of them. > Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] from > m2. > > I tried several combinations of "load" and "select", but no option worked. > The last selection is always applied to both molecules. I also Googled it, > without any success. > > Does anyone know if its possible to make a selection in isolation over a > given molecule? > Any suggestion will be highly appreciated! > > Thanks in advance, > Alessia > -- > 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=58041391&iu=/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=58041391&iu=/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
[PyMOL] Select different set of atoms in different molecules
Dear pyMOL users, I'm puzzled about how to solve an apparently simple task. I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select two different sets of atoms from each of them. Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] from m2. I tried several combinations of "load" and "select", but no option worked. The last selection is always applied to both molecules. I also Googled it, without any success. Does anyone know if its possible to make a selection in isolation over a given molecule? Any suggestion will be highly appreciated! Thanks in advance, Alessia -- 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=58041391&iu=/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] Select different set of atoms in different molecules
It helped a lot, thank you very much. Alessia On 5 September 2013 22:20, Bernhard Lechtenberg < blechtenb...@sanfordburnham.org> wrote: > Hi Allesia, > > I am not quite sure how to want to select the atoms, but if you want to > have the selected atoms of both m1 and m2 in the same selection (here s1), > then try this: > select s1, (m1 and id 1-3) or (m2 and id 7-9) > > if you want two different selections, just do > select s1, m1 and id 1-3 > select s2, m2 and id 7-9 > > Hope that helps, > Bernhard > > On Sep 5, 2013, at 12:40 PM, Alessia Visconti > wrote: > > > Dear pyMOL users, > > I'm puzzled about how to solve an apparently simple task. > > > > I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select > two different sets of atoms from each of them. > > Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] > from m2. > > > > I tried several combinations of "load" and "select", but no option > worked. > > The last selection is always applied to both molecules. I also Googled > it, without any success. > > > > Does anyone know if its possible to make a selection in isolation over a > given molecule? > > Any suggestion will be highly appreciated! > > > > Thanks in advance, > > Alessia > > > -- > > 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=58041391&iu=/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=58041391&iu=/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=58040911&iu=/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=58041391&iu=/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] set line_width command doesn't work
Hi Yeping, I confirm that this is broken is 1.5, but works fine in 1.6. It seems that this was a bug in the early version of the lines shader. So until you have the change to upgrade, I suggest to disable the line shader: PyMOL> unset line_use_shader Cheers, Thomas sunyeping wrote, On 09/04/13 17:21: > Dear all > > I want to make line presentation in pymol looks more thicker so I enter > "set line_width, 3", but the lines in the viewer window don't show any > change. Have you meet such circumstance? The pymol (version 1.5.0.1) is > installed in centos5.9 system and other functions seem well. Thanks. > > Yeping Sun > > Institute of Microbiology, Chinese Academy of Sciences -- 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=58041391&iu=/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
