[chimerax-users] scale bar in chimerax

[Xu 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 at cgl.ucsf.edu]
Sent: Thursday, December 13, 2018 10:45 PM
To: Xu  Jingwei
Cc: chimerax-users at 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 at 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