[chimerax-users] scale_bar
Tom Goddard goddard at sonic.net
Fri Jul 9 18:37:55 PDT 2021
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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 at 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 at 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 at 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 at 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 at 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 at cgl.ucsf.edu >> Manage subscription: >> https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users >>>>> _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users at cgl.ucsf.edu > Manage subscription: > https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210709/48549e02/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: image1.png Type: image/png Size: 466342 bytes Desc: not available URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210709/48549e02/attachment-0001.png>