to our friendly developer, Is there a way to specify the physical size for a view, so that different sized molecule or map is shown at the same physical scale from different sessions. By the way, is there a command to specify the pixel size of the window? the shrink to fit or grow to fit doesn't work well. many thanks! Jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>< Jinghua Tang, Ph.D. Phone: 858-534-5852(o) 4107 Natural Sciences Bldg, MC-0378 858-597-2056(h) Department of Chemistry & Biochemistry Fax: 858-534-5846 University of California, San Diego E-mail: jinghua@ucsd.edu La Jolla, CA 92093-0378 http://cryoem.ucsd.edu/~jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><
Hi Jinghua, Below is some Python code which adds two Chimera commands: setzoom <pixels-per-angstrom> windowsize <width-in-pixels> <height-in-pixels> Put it in a file in your Chimera distribution chimera/share/zoom/ChimeraExtension.py You'll need to make the directory zoom (directory name does not matter). There are some problems with these commands to be aware of. The setzoom command works correctly in orthographic camera mode, but not perspective camera mode. Use Favorites / Side View and switch to the Camera tab and choose Projection: orthographic. In perspective mode objects closer to you eye appear bigger. I tried to make the code set the pixels per angstrom at a depth equal to the center of the bounding box of your displayed models. But by using the Chimera Scalebar tool I can see it is not quite right. By the way, you can use the Chimera Scalebar tool (Tools / Utilities / Scalebar) to hand adjust the zoom to a standard size. You make the scale bar the width you want for the full window, move it to center it, then zoom until it just touches the edges of the window. Kind of tedious. The windowsize command won't make the window have small horizontal widths (less than about 400 pixels) if the command-line or status-line are being displayed. You can hide the status line using the Favorites / Preferences / Messages / Show status line switch. You can hide the command line with Tools / Command Line / hide. You can still type commands with the command-line hidden. We'll try to include some better working versions of these commands in a future release. Tom ----- zoom/ChimeraExtension.py follows: # --------------------------------------------------------------------------- # The status line and command entry box at the bottom of the main Chimera # window prevent the window from being resized by this code to a width # smaller than about 450 pixels. The status line can be turned off using # Favorites / Preferences / Messages / Show status line, and the command-line # can be hidden with Tools / Command-line / hide. Commands can still be # typed with the command-line hidden. # def set_window_size(cmd_name, args): try: width, height = map(int, args.split()) except: from Midas.midas_text import error error('Syntax error: %s <width-in-pixels> <height-in-pixels>' % cmd_name) import chimera v = chimera.viewer v.windowSize = (width, height) # # If user resizes the main window by hand the above size will not take # effect unless we reset top level geometry. # from chimera import tkgui app = tkgui.app top = app.winfo_toplevel() top.wm_geometry('') # --------------------------------------------------------------------------- # def set_camera_zoom(cmd_name, args): try: pixels_per_angstrom = float(args) except: from Midas.midas_text import error error('Syntax error: %s <pixels-per-angstrom>' % cmd_name) import chimera have_bbox, bbox = chimera.openModels.bbox() if not have_bbox: return v = chimera.viewer width, height = v.windowSize # window size in pixels min_size = min(width,height) r = .5 * min_size / pixels_per_angstrom v.viewSize = r v.scaleFactor = 1 v.camera.focal = bbox.center().z # --------------------------------------------------------------------------- # import Midas.midas_text Midas.midas_text.addCommand('windowsize', set_window_size) Midas.midas_text.addCommand('setzoom', set_camera_zoom)
Hi Jinghua, I made a couple corrections to the code I sent in the previous email so that if the command arguments are incorrect an error message is properly reported. Tom --- zoom/ChimeraExtension.py follows: # --------------------------------------------------------------------------- # The status line and command entry box at the bottom of the main Chimera # window prevent the window from being resized by this code to a width # smaller than about 450 pixels. The status line can be turned off using # Favorites / Preferences / Messages / Show status line, and the command-line # can be hidden with Tools / Command-line / hide. Commands can still be # typed with the command-line hidden. # def set_window_size(cmd_name, args): try: width, height = map(int, args.split()) except: from Midas import MidasError raise MidasError, 'Syntax error: %s <width-in-pixels> <height-in-pixels>' % cmd_name import chimera v = chimera.viewer v.windowSize = (width, height) # # If user resizes the main window by hand the above size will not take # effect unless we reset top level geometry. # from chimera import tkgui app = tkgui.app top = app.winfo_toplevel() top.wm_geometry('') # --------------------------------------------------------------------------- # def set_camera_zoom(cmd_name, args): try: pixels_per_angstrom = float(args) except: from Midas import MidasError raise MidasError, 'Syntax error: %s <pixels-per-angstrom>' % cmd_name import chimera have_bbox, bbox = chimera.openModels.bbox() if not have_bbox: return v = chimera.viewer width, height = v.windowSize # window size in pixels min_size = min(width,height) r = .5 * min_size / pixels_per_angstrom v.viewSize = r v.scaleFactor = 1 v.camera.focal = bbox.center().z # --------------------------------------------------------------------------- # import Midas.midas_text Midas.midas_text.addCommand('windowsize', set_window_size) Midas.midas_text.addCommand('setzoom', set_camera_zoom)
participants (2)
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jinghua＠ucsd.edu -
Thomas Goddard