Hi, First of all, this is a great program, and I am barely using it to full extent of its possibilities. I am currently interested in combining a 3D object (a molecule.pdb) and a 2D object/plane/image (as a .png or any other). The idea being that I want to show a slice of an ELF plot, with the 3D molecule embedded through the 2D plot. Good news is that I can import both objects (.pdb and .png). However I face a size issue with the 2D object, which is considerably bigger than the 3D one. Would you know if I can size down a 2D object, or enlarge a 3D one respectively. All in all would you know if chimeraX can generate something like the picture attached by combining a 2D and a 3D object. Thanks for your time, Cheers, Rodolphe [cid:D31DAF51-91B8-4F78-94B3-4C0FCD9C860E] Dr. Rodolphe Jazzar, CNRS Research Associate - (French National Centre for Scientific Research) UCSD-UMI 3555 ORCID : 0000-0002-4156-7826 Office: (858)-534-5315 Mobile: 858-337-2228 University of California, San Diego, 5213 Pacific Hall, Department of Chemistry, 9500 Gilman Dr, # 0343, La Jolla, CA 92093-0343 http://bertrandgroup.ucsd.edu<http://bertrandgroup.ucsd.edu/> https://northamerica.cnrs.fr<https://northamerica.cnrs.fr/> http://www.cnrs.fr/en/cnrs [cid:image001.png@01CFDE12.00855770]
Hi Rodolphe, Glad you like it! If your color PNG can be opened in ChimeraX, it thinks it is "volume data" even though it is really 2D. In that case you can use the "volume" command "voxelSize" option to change its scale relative to any atomic structures, and you can also move and rotate it relative to those structures (or vice versa). E.g. if the PNG is open as model #1, a command something like: volume #1 voxelSize 0.5 ...you'd have to play around with the size and see what works. The molecules can be in any location relative to this flat "volume" model, including interpenetrating. You can move the models separately, e.g. by Ctrl-click selection and using "move selected" mouse modes, or by directly specifying any of the model(s) as those to move in "move" and "turn" commands. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/turn.html> In our older program Chimera, you can use a color image (PNG, others) as the window background (Favorites... Preferences, Category Background), then zoom in and out on the structure(s) to adjust their size relative to the background. However, using an image from file as the background is not yet implemented in ChimeraX. An all-in-one approach if the ELF were available in on of the 3D volume formats known to ChimeraX (and Chimera) could be to open that 3D data and do the slicing and coloring by ELF value in ChimeraX as well. However, only Chimera (not yet ChimeraX) currently allows slicing the volume without also slicing the structure(s). At first I thought color PNGs could not be opened in ChimeraX because when I tried one example, I got a message "image mode RGBA is not supported." I'd thought that image stacks were grayscale only. Luckily my coworker told me that it does indeed work for at least some color PNGs. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 4, 2020, at 2:03 PM, Jazzar, Rodolphe <rjazzar@UCSD.EDU> wrote:
Hi, First of all, this is a great program, and I am barely using it to full extent of its possibilities. I am currently interested in combining a 3D object (a molecule.pdb) and a 2D object/plane/image (as a .png or any other). The idea being that I want to show a slice of an ELF plot, with the 3D molecule embedded through the 2D plot. Good news is that I can import both objects (.pdb and .png). However I face a size issue with the 2D object, which is considerably bigger than the 3D one. Would you know if I can size down a 2D object, or enlarge a 3D one respectively. All in all would you know if chimeraX can generate something like the picture attached by combining a 2D and a 3D object.
Thanks for your time, Cheers, Rodolphe
<Capture d’écran 2020-06-03 à 23.04.20.png>
HI Rodolphe, To add a little to Elaine's suggestions, ChimeraX will open your PNG as if it were three channel microscopy data (if the PNG has RGB pixels). That is a bit weird. It will set the brightness profiles of the 3 color components in a weird way appropriate for microscopy data although you could make it appear like the original image by making the yellow line brightness curves on the 3 histograms straight lines. Tom
On Jun 4, 2020, at 3:32 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Rodolphe, Glad you like it!
If your color PNG can be opened in ChimeraX, it thinks it is "volume data" even though it is really 2D. In that case you can use the "volume" command "voxelSize" option to change its scale relative to any atomic structures, and you can also move and rotate it relative to those structures (or vice versa). E.g. if the PNG is open as model #1, a command something like:
volume #1 voxelSize 0.5
...you'd have to play around with the size and see what works.
The molecules can be in any location relative to this flat "volume" model, including interpenetrating. You can move the models separately, e.g. by Ctrl-click selection and using "move selected" mouse modes, or by directly specifying any of the model(s) as those to move in "move" and "turn" commands. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/turn.html>
In our older program Chimera, you can use a color image (PNG, others) as the window background (Favorites... Preferences, Category Background), then zoom in and out on the structure(s) to adjust their size relative to the background. However, using an image from file as the background is not yet implemented in ChimeraX.
An all-in-one approach if the ELF were available in on of the 3D volume formats known to ChimeraX (and Chimera) could be to open that 3D data and do the slicing and coloring by ELF value in ChimeraX as well. However, only Chimera (not yet ChimeraX) currently allows slicing the volume without also slicing the structure(s).
At first I thought color PNGs could not be opened in ChimeraX because when I tried one example, I got a message "image mode RGBA is not supported." I'd thought that image stacks were grayscale only. Luckily my coworker told me that it does indeed work for at least some color PNGs.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 4, 2020, at 2:03 PM, Jazzar, Rodolphe <rjazzar@UCSD.EDU> wrote:
Hi, First of all, this is a great program, and I am barely using it to full extent of its possibilities. I am currently interested in combining a 3D object (a molecule.pdb) and a 2D object/plane/image (as a .png or any other). The idea being that I want to show a slice of an ELF plot, with the 3D molecule embedded through the 2D plot. Good news is that I can import both objects (.pdb and .png). However I face a size issue with the 2D object, which is considerably bigger than the 3D one. Would you know if I can size down a 2D object, or enlarge a 3D one respectively. All in all would you know if chimeraX can generate something like the picture attached by combining a 2D and a 3D object.
Thanks for your time, Cheers, Rodolphe
<Capture d’écran 2020-06-03 à 23.04.20.png>
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participants (3)
-
Elaine Meng -
Jazzar, Rodolphe -
Tom Goddard