[chimerax-users] Scale bar in ChimeraX

[Stapleton kevin2017/4/3]

Anindito Sen,

Hey man I have a kinda long work around this problem but it works.

#Example case:
open 22296 from emdb


### Under the   "medical Image"   tab on the top of the gui, click on the   "tape"   button on the far right.  Command to do this is below:
ui mousemode right "tape measure"

### Using the right click of your mouse, if you R-click on the edge of your volume, hold-and-drag the mouse you will get a distance in Angstroms of the line you are drawing. Releasing the R-click will place the line in your view. The command log should leave you with something like this:

marker segment #2 position 79.46,34.11,51.34 toPosition 101.3,34.51,54.39 color yellow radius 0.205 label 22.03 labelHeight 2.203 labelColor yellow

### If you want to play with these paramiters in chimeraX here is the breakdown of what the command line is doing:

marker segment #[ID in the models window] position [start point] to Position [finish point] color [any color you want] radius [thickness of the line drawn] label 22.03 labelHeight [font size essentially] labelColor [color the letters]

*** note:  the measure appears to require you to start by clicking on an atom or volume.  To redraw this in a position you like you could play with the   "position [start point] to Position [finish point] " but that takes a lot of playing time.  So to avoid this, I save the image with and without the scale

### Show scale
show #!2 models
save ~/Desktop/with_scale.png supersample 3 transparentbackground tru

### No scale
hide #!2 models
save ~/Desktop/no_scale.png supersample 3 transparentbackground tru

### Lastly, open you favourite photo editing program and open your with_scale.png.  Draw a line over the length of the existing one, edit to your liking (color, text, position etc..), and copy past it into your no-scale.png

This looks like it takes a while to do, but its pretty quick once you try it once.  

Hope this helps :-)

All the best,
Kako






----- Original Message -----
>> From: Sen, Anindito <andysen at tamu.edu>
>> To: "chimerax-users at cgl.ucsf.edu" <chimerax-users at cgl.ucsf.edu>
>> Date: 2021-04-27 08:27:04
>> Subject: [chimerax-users] Scale bar in ChimeraX
>> 
>> Dear All,
>> 
>> How to put a scale bar in a ChimeraX session depicting a density map ( as in Chimera Tools -  High-Order structure -Scale Bar).
>> 
>> Stay safe & Regards
>> 
>> Anindito Sen. Ph.D
>> 
>> Microscopy and Imaging Center
>> Texas A&M University
>> 301 Old Main Dr
>> College Station, TX 77843-2257
>> 
>> Office: ILSB Room 1133
>> <http://microscopy.tamu.edu/>Tel. 979-458-9881
>> fax: 979-847-8933
>> http://microscopy.tamu.edu<http://microscopy.tamu.edu/>
>> 
>> 
>> 
>>