From: Gudrun L. <gud...@gm...> - 2012-02-27 10:38:20
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Dear all, is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please? I have a protein made from dummy atoms and there is no unit cell. I just want to show clearly which plane is shown when presenting the model in my document. Thank you for your help. Kind regards Gudrun Lotze |
From: David H. <li...@co...> - 2012-02-27 12:24:59
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http://pymolwiki.org/index.php/Axes -David On Feb 27, 2012, at 5:38 AM, Gudrun Lotze <gud...@gm...> wrote: > Dear all, > > is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please? > I have a protein made from dummy atoms and there is no unit cell. > I just want to show clearly which plane is shown when presenting the model in my document. > > Thank you for your help. > Kind regards > Gudrun Lotze > > > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Gudrun L. <gud...@gm...> - 2012-02-27 12:37:08
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Dear all, I used the following script David pointed out: from pymol.cgo import * from pymol import cmd w = 0.06 # cylinder width l = 0.75 # cylinder length h = 0.25 # cone hight d = w * 1.618 # cone base diameter obj = [CYLINDER, 0.0, 0.0, 0.0, l, 0.0, 0.0, w, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, CYLINDER, 0.0, 0.0, 0.0, 0.0, l, 0.0, w, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, CYLINDER, 0.0, 0.0, 0.0, 0.0, 0.0, l, w, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, CONE, l, 0.0, 0.0, h+l, 0.0, 0.0, d, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, CONE, 0.0, l, 0.0, 0.0, h+l, 0.0, d, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0, CONE, 0.0, 0.0, l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0] cmd.load_cgo(obj, 'axes') The axes appear, but the screen in pymol is now split into two sections with the cross covering one part. Is there a chance to move the cross closer to the model in one screen section? A bit like shown in picture on page http://pymolwiki.org/index.php/Axes . Kind regards Gudrun Am 27.02.2012 um 12:01 schrieb David Hall: > http://pymolwiki.org/index.php/Axes > > -David > > On Feb 27, 2012, at 5:38 AM, Gudrun Lotze <gud...@gm...> wrote: > >> Dear all, >> >> is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please? >> I have a protein made from dummy atoms and there is no unit cell. >> I just want to show clearly which plane is shown when presenting the model in my document. >> >> Thank you for your help. >> Kind regards >> Gudrun Lotze >> >> >> ------------------------------------------------------------------------------ >> Try before you buy = See our experts in action! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-dev2 >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... |
From: Thomas H. <sp...@us...> - 2012-02-27 12:50:46
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Hi Gudrun, On 02/27/2012 01:36 PM, Gudrun Lotze wrote: > The axes appear, but the screen in pymol is now split into two sections > with the cross covering one part. Is there a chance to move the cross > closer to the model in one screen section? > A bit like shown in picture on page http://pymolwiki.org/index.php/Axes . You can drag the axes object with the mouse. In the right panel, click on "A > drag" and then use Shift+MiddleMouseButton to drag it. If you prefer the command line over mouse, you could use translate and rotate commands: http://pymolwiki.org/index.php/Translate http://pymolwiki.org/index.php/Rotate Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Thomas H. <sp...@us...> - 2012-02-27 14:58:10
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Dear Gudrun, I have no experience with PyMOL on Mac. Maybe this helps: http://pymolwiki.org/index.php/Mouse_Controls Deselecting objects does not help, because by default you transform in camera space, which affects all objects. What you need is transformation in model space, which is achieved by "A > drag" or "A > drag matrix" for a particular object. Here an example to use the command line: translate [10,0,0], object=axes Hope that helps. Cheers, Thomas On 02/27/2012 03:21 PM, Gudrun Lotze wrote: > Dear Thomas Thank you for your reply. The mouse dragging does not > work because the Mac starts to move windows in a very beautiful way > which I never came across. :-) So I used a 2-button mouse. But there > is still a problem. The dummy atom model and the three axes object > are always moving together when dragging around. Even when I deselect > the model, drag the cross, and re-select the model, the model has > moved as well. May I have to shift the cross within the script? > > Kind regards Gudrun > > Am 27.02.2012 um 12:50 schrieb Thomas Holder: > >> Hi Gudrun, >> >> On 02/27/2012 01:36 PM, Gudrun Lotze wrote: >>> The axes appear, but the screen in pymol is now split into two >>> sections with the cross covering one part. Is there a chance to >>> move the cross closer to the model in one screen section? A bit >>> like shown in picture on page http://pymolwiki.org/index.php/Axes >>> . >> >> You can drag the axes object with the mouse. In the right panel, >> click on "A> drag" and then use Shift+MiddleMouseButton to drag >> it. >> >> If you prefer the command line over mouse, you could use translate >> and rotate commands: http://pymolwiki.org/index.php/Translate >> http://pymolwiki.org/index.php/Rotate >> >> Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |