Hi, I recently installed the ChimeraX in my centos 7 and it is really powerful software to make beautiful figures. I really like it! However, one question before I setup for figures is how could I make a scale bar in ChimeraX? I did not find the relative information in the web. Could you please help me about that? I am really appreciated for that. Best, Jingwei ETH Zürich Dr. Jingwei Xu Postdoc Institute of Molecular Biology & Biophysics Department of Biology HPK D17 Otto-Stern-Weg 5 8093 Zürich, Switzerland
Hi Jingwei, Sorry, there is no Scale Bar tool in ChimeraX currently. You could create a 3D object of the desired length but you would have to position it carefully in the same plane as your other structure(s) and in a horizontal orientation, and then add the label on it with the “2dlabel” command. Ways to create the 3D object are all by generating a file and reading it in: (1) read in a BILD file that defines a cylinder of the desired length <http://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html> … this file could be very simple, for example just containing one line of text: .cylinder 0 0 0 0 0 20 1 (values are x1 y1 z1 x2 y2 z2 radius) (2) read in a PDB file with two atoms the desired distance apart and bond between them (3) read in a marker file with two markers the desired distance apart and link between them <http://rbvi.ucsf.edu/chimerax/docs/user/markers.html#markerfiles> A different approach is to save the image with a specific pixelSize per physical distance and then use some image-editing app to add a bar of the desired number of pixels and its label. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 13, 2018, at 5:54 AM, Xu Jingwei <jingwei.xu@mol.biol.ethz.ch> wrote:
Hi, I recently installed the ChimeraX in my centos 7 and it is really powerful software to make beautiful figures. I really like it! However, one question before I setup for figures is how could I make a scale bar in ChimeraX? I did not find the relative information in the web. Could you please help me about that? I am really appreciated for that.
Best,
Jingwei
Thanks, Elaine. Your suggestions are really helpful. I will try it later. Best, Jingwei ETH Zürich Dr. Jingwei Xu Postdoc Institute of Molecular Biology & Biophysics Department of Biology HPK D17 Otto-Stern-Weg 5 8093 Zürich, Switzerland ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, December 13, 2018 10:45 PM To: Xu Jingwei Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] scale bar in chimerax Hi Jingwei, Sorry, there is no Scale Bar tool in ChimeraX currently. You could create a 3D object of the desired length but you would have to position it carefully in the same plane as your other structure(s) and in a horizontal orientation, and then add the label on it with the “2dlabel” command. Ways to create the 3D object are all by generating a file and reading it in: (1) read in a BILD file that defines a cylinder of the desired length <http://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html> … this file could be very simple, for example just containing one line of text: .cylinder 0 0 0 0 0 20 1 (values are x1 y1 z1 x2 y2 z2 radius) (2) read in a PDB file with two atoms the desired distance apart and bond between them (3) read in a marker file with two markers the desired distance apart and link between them <http://rbvi.ucsf.edu/chimerax/docs/user/markers.html#markerfiles> A different approach is to save the image with a specific pixelSize per physical distance and then use some image-editing app to add a bar of the desired number of pixels and its label. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 13, 2018, at 5:54 AM, Xu Jingwei <jingwei.xu@mol.biol.ethz.ch> wrote:
Hi, I recently installed the ChimeraX in my centos 7 and it is really powerful software to make beautiful figures. I really like it! However, one question before I setup for figures is how could I make a scale bar in ChimeraX? I did not find the relative information in the web. Could you please help me about that? I am really appreciated for that.
Best,
Jingwei
participants (2)
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Elaine Meng -
Xu Jingwei