Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong
On May 7, 2008, at 11:18 PM, Yao Cong wrote:
Hello Chimera developer,
I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used?
Hi Yao, There's no way to do this directly in Chimera now, though I am working on a tool that will make it easy to produce such a key -- but it's not ready yet. For now you will have to use an external image- processing program such as GIMP or photoshop to add the key. There is some basic advice for doing this in this message: http:// www.cgl.ucsf.edu/pipermail/chimera-users/2006-July/000878.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Dear Chimera developer, I am trying to install the daily released Chimera (July 15, 2009) in a 64bit Linux, and it shows the following error message. I also list my Linux system below. Could you give me some suggestion on what I should do to fix it? Thanks, Yao ~~~~~~~~~~~ [ycong@panda bin]$ chimera Traceback (most recent call last): File "/app/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/app/chimera/share/chimeraInit.py", line 374, in init tkgui.initializeGUI(exitonquit, debug_opengl) File "CHIMERA/share/chimera/tkgui.py", line 2666, in initializeGUI File "/app/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 322, in checkConfig File "/app/chimera/lib/python2.5/site-packages/Togl.py", line 27, in __init__ Tkinter.Widget.__init__(self, master, "togl", cnf, kw) File "/app/chimera/lib/python2.5/lib-tk/Tkinter.py", line 1930, in __init__ (widgetName, self._w) + extra + self._options(cnf)) _tkinter.TclError: couldn't choose pixel format Couldn't configure togl widget My Linux system is: Linux name.bcm.edu 2.6.27.12-170.2.5.fc10.x86_64 #1 SMP Wed Jan 21 01:33:24 EST 2009 x86_64 x86_64 x86_64 GNU/Linux
Hi Yao (and chimera-users), The error message should have read: Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions. The other common error on Linux is that your OpenGL configuration got messed up when you updated your system. For example, if you previously had a NVidia or ATI graphics driver installed, then updated your system from Fedora 10 to Fedora 11, then the updated system might be in an inconsistent state until you reinstalled the NVidia or ATI driver. If /usr/bin/glxgears works (in the glx-utils package) and chimera doesn't, then please let me know and we'll dig into this deeper. Greg On Thu, 16 Jul 2009, Yao Cong wrote:
Dear Chimera developer,
I am trying to install the daily released Chimera (July 15, 2009) in a 64bit Linux, and it shows the following error message. I also list my Linux system below. Could you give me some suggestion on what I should do to fix it?
Thanks,
Yao
~~~~~~~~~~~ [ycong@panda bin]$ chimera Traceback (most recent call last): File "/app/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/app/chimera/share/chimeraInit.py", line 374, in init tkgui.initializeGUI(exitonquit, debug_opengl) File "CHIMERA/share/chimera/tkgui.py", line 2666, in initializeGUI File "/app/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 322, in checkConfig
File "/app/chimera/lib/python2.5/site-packages/Togl.py", line 27, in __init__ Tkinter.Widget.__init__(self, master, "togl", cnf, kw) File "/app/chimera/lib/python2.5/lib-tk/Tkinter.py", line 1930, in __init__ (widgetName, self._w) + extra + self._options(cnf)) _tkinter.TclError: couldn't choose pixel format Couldn't configure togl widget
My Linux system is: Linux name.bcm.edu 2.6.27.12-170.2.5.fc10.x86_64 #1 SMP Wed Jan 21 01:33:24 EST 2009 x86_64 x86_64 x86_64 GNU/Linux
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participants (3)
-
Eric Pettersen -
Greg Couch -
Yao Cong