Hi Dmitry, ChimeraX does not yet have a scale bar. It is listed in the "Missing Features" section on the download page. <https://www.rbvi.ucsf.edu/chimerax/download.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2021, at 11:03 AM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues, Quick question – would you be so kind and tell me where the scale bar can be found? Thanks Sincerely, Dmitry
Hi Dmitry, There may not be a good workaround. Some (inconvenient and/or difficult) possibilities in ChimeraX have been discussed in previous posts. Making a 3D object with simple BILD format, or using a specific pixel size per distance to create the image and then using some separate image-editing program to add a scale bar: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-December/000341.html> Using "shape rectangle" to make a planar rectangle of specified size, but it could be very difficult to position it exactly right: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001899.html> You can draw a horizontal bar by hand using the Color Key tool (just make it all one color) but you would have to figure out the scaling yourself and enter in the numbers manually. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorkey.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2021, at 12:27 PM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thanks, I see.
And what is the walk around strategy? )
Sincerely, Dmitry
From: Elaine Meng Sent: Thursday, July 8, 2021 8:14 PM To: Dmitry A. Semchonok Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] scale_bar
Hi Dmitry, ChimeraX does not yet have a scale bar. It is listed in the "Missing Features" section on the download page.
<https://www.rbvi.ucsf.edu/chimerax/download.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2021, at 11:03 AM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues, Quick question – would you be so kind and tell me where the scale bar can be found? Thanks Sincerely, Dmitry
Hi Dmitry, One other method for making a scale bar which I think is the easiest is to set the ChimeraX zoom by specifying the screen image pixel size in Angstroms with ChimeraX command zoom pixelSize 0.5 Then save your image without changing the zoom and add a scale bar with an image editor (Photoshop, Gimp, ...). If I wanted a 50 Angstrom scale bar I would make a 100 pixel wide rectangle in the photo editor since each pixel is 0.5 Angstroms. Keep in mind with perspective projection the pixel size varies with the depth and the zoom command sets the pixel size at the depth of the center of rotation. You may want to use orthographic projection so the pixel size does not vary with depth, ChimeraX command camera ortho Tom
On Jul 8, 2021, at 1:21 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry, There may not be a good workaround.
Some (inconvenient and/or difficult) possibilities in ChimeraX have been discussed in previous posts.
Making a 3D object with simple BILD format, or using a specific pixel size per distance to create the image and then using some separate image-editing program to add a scale bar: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-December/000341.html>
Using "shape rectangle" to make a planar rectangle of specified size, but it could be very difficult to position it exactly right: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001899.html>
You can draw a horizontal bar by hand using the Color Key tool (just make it all one color) but you would have to figure out the scaling yourself and enter in the numbers manually. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorkey.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2021, at 12:27 PM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thanks, I see.
And what is the walk around strategy? )
Sincerely, Dmitry
From: Elaine Meng Sent: Thursday, July 8, 2021 8:14 PM To: Dmitry A. Semchonok Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] scale_bar
Hi Dmitry, ChimeraX does not yet have a scale bar. It is listed in the "Missing Features" section on the download page.
<https://www.rbvi.ucsf.edu/chimerax/download.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2021, at 11:03 AM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues, Quick question – would you be so kind and tell me where the scale bar can be found? Thanks Sincerely, Dmitry
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Tom and Elaine, Thanks a lot for the suggestions. I need to try them. Dear Elaine One more small question - If general USCF Chimera has the same nice option (pre-sets) such as Publication-Quality Images in ChimeraX with pressing just few buttons? Thank you Sincerely, Dmitry
On 9. Jul 2021, at 02:23, Tom Goddard <goddard@sonic.net> wrote:
Hi Dmitry,
One other method for making a scale bar which I think is the easiest is to set the ChimeraX zoom by specifying the screen image pixel size in Angstroms with ChimeraX command
zoom pixelSize 0.5
Then save your image without changing the zoom and add a scale bar with an image editor (Photoshop, Gimp, ...). If I wanted a 50 Angstrom scale bar I would make a 100 pixel wide rectangle in the photo editor since each pixel is 0.5 Angstroms.
Keep in mind with perspective projection the pixel size varies with the depth and the zoom command sets the pixel size at the depth of the center of rotation. You may want to use orthographic projection so the pixel size does not vary with depth, ChimeraX command
camera ortho
Tom
On Jul 8, 2021, at 1:21 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry, There may not be a good workaround.
Some (inconvenient and/or difficult) possibilities in ChimeraX have been discussed in previous posts.
Making a 3D object with simple BILD format, or using a specific pixel size per distance to create the image and then using some separate image-editing program to add a scale bar: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-December/000341.html>
Using "shape rectangle" to make a planar rectangle of specified size, but it could be very difficult to position it exactly right: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001899.html>
You can draw a horizontal bar by hand using the Color Key tool (just make it all one color) but you would have to figure out the scaling yourself and enter in the numbers manually. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorkey.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2021, at 12:27 PM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thanks, I see.
And what is the walk around strategy? )
Sincerely, Dmitry
From: Elaine Meng Sent: Thursday, July 8, 2021 8:14 PM To: Dmitry A. Semchonok Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] scale_bar
Hi Dmitry, ChimeraX does not yet have a scale bar. It is listed in the "Missing Features" section on the download page.
<https://www.rbvi.ucsf.edu/chimerax/download.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2021, at 11:03 AM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues, Quick question – would you be so kind and tell me where the scale bar can be found? Thanks Sincerely, Dmitry
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Dmitry, It's almost the same as in Chimera. ChimeraX menu: Presets... Overall Look... Publication, or command: preset pub The result is also about the same as in Chimera. However, ChimeraX has all kinds of additional features like fancier lighting and curved-cylinder (tube) helices, so you may also want to try the different lighting icons in the Toolbar, other options in the Presets menu (e.g. those under Presets... Cartoons/Nucleotides...) etc. All the presets are described here, and you can also create your own custom presets: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.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 Jul 9, 2021, at 12:20 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine
One more small question - If general USCF Chimera has the same nice option (pre-sets) such as Publication-Quality Images in ChimeraX with pressing just few buttons? Thank you
Sincerely, Dmitry
Hi Dmitry, I added a "scalebar" command to ChimeraX, in tonight's daily builds. To make a scalebar 10 Angstroms long scalebar 10 and here are examples changing its color, position, size. scalebar color blue xpos .7 scalebar color auto scalebar 50 thickness 5 scalebar off It adjusts size as you zoom. Also the "move label" mouse mode lets you drag the scalebar to a new position. The scale bar is a special kind of 2D label. Unlike Chimera it does not show a number over the label and there is not yet a user interface panel for it, just the command. Tom
On Jul 8, 2021, at 5:23 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry,
One other method for making a scale bar which I think is the easiest is to set the ChimeraX zoom by specifying the screen image pixel size in Angstroms with ChimeraX command
zoom pixelSize 0.5
Then save your image without changing the zoom and add a scale bar with an image editor (Photoshop, Gimp, ...). If I wanted a 50 Angstrom scale bar I would make a 100 pixel wide rectangle in the photo editor since each pixel is 0.5 Angstroms.
Keep in mind with perspective projection the pixel size varies with the depth and the zoom command sets the pixel size at the depth of the center of rotation. You may want to use orthographic projection so the pixel size does not vary with depth, ChimeraX command
camera ortho
Tom
On Jul 8, 2021, at 1:21 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry, There may not be a good workaround.
Some (inconvenient and/or difficult) possibilities in ChimeraX have been discussed in previous posts.
Making a 3D object with simple BILD format, or using a specific pixel size per distance to create the image and then using some separate image-editing program to add a scale bar: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-December/000341.html>
Using "shape rectangle" to make a planar rectangle of specified size, but it could be very difficult to position it exactly right: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001899.html>
You can draw a horizontal bar by hand using the Color Key tool (just make it all one color) but you would have to figure out the scaling yourself and enter in the numbers manually. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorkey.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2021, at 12:27 PM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thanks, I see.
And what is the walk around strategy? )
Sincerely, Dmitry
From: Elaine Meng Sent: Thursday, July 8, 2021 8:14 PM To: Dmitry A. Semchonok Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] scale_bar
Hi Dmitry, ChimeraX does not yet have a scale bar. It is listed in the "Missing Features" section on the download page.
<https://www.rbvi.ucsf.edu/chimerax/download.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2021, at 11:03 AM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues, Quick question – would you be so kind and tell me where the scale bar can be found? Thanks Sincerely, Dmitry
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
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Dmitry A. Semchonok -
Dmitry Semchonok
-
Elaine Meng -
Tom Goddard