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/>
Hi Anindito, Sorry there is no Scale Bar tool in ChimeraX currently... I should probably add that to the "missing features" list in the download page. This older post has some suggestions for possible workarounds: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-December/000341.html> Stay safe & regards to you too, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 26, 2021, at 4:27 PM, Sen, Anindito <andysen@tamu.edu> wrote:
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
Additionally Elaine, What will be the process to get the lighting option in ChimeraX as in Chimera (Favorites- side view-Lighting) 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/> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, April 26, 2021 6:34 PM To: Sen, Anindito Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Scale bar in ChimeraX Hi Anindito, Sorry there is no Scale Bar tool in ChimeraX currently... I should probably add that to the "missing features" list in the download page. This older post has some suggestions for possible workarounds: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/pipermail/chimerax-use... > Stay safe & regards to you too, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 26, 2021, at 4:27 PM, Sen, Anindito <andysen@tamu.edu> wrote:
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
Hi Anindito, Lighting is very different in ChimeraX than in Chimera. ChimeraX has several Toolbar icons to apply different lighting options in a single click. Maybe you wanted to change the lighting directions? In that case, since ChimeraX does not have a Lighting GUI currently, you would have to use the "lighting" command, e.g. with options "direction" and "fillDirection." The lighting icons and command options are explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 26, 2021, at 10:14 PM, Sen, Anindito <andysen@tamu.edu> wrote:
Additionally Elaine, What will be the process to get the lighting option in ChimeraX as in Chimera (Favorites- side view-Lighting) Stay safe & Regards Anindito Sen. Ph.D
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@tamu.edu> To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@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/>
participants (3)
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Elaine Meng -
Sen, Anindito -
Stapleton kevin2017/4/3