Hi Christoph, The transparent background option for saving an image worked fine for me on a Mac save image ~/Desktop/test.png transparentBackground true To set the absolute zoom level zoom pixelsize .05 sets each pixel to be .05 Angstroms. ChimeraX has detailed documentation http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image> http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html> Tom

On Jul 31, 2018, at 1:12 AM, Christoph Bachmann wrote:

Dear ChimeraX team

First of all, great piece of software. It’s a lot more userfriendly than pyMol or VMD. But it is hard to find information, since most is still for the old Chimera.

I’m struggeling to get transparency in saved pngs to work. I’ve tried it on a PC and a Mac with no luck. This is strange since both computers support transparency and I regularly work with that feature so it can’t be a hardware problem.

My main question is how to get absolute sizes of the molecules. I’m currently making an illustration with different molecules, from small to large and I want their size to be displayed as accurate as possible (so a carbon atom in one molecule is exactly as big as the one in another molecule). I’m sure there is an easy way but I haven’t found anything so far. If I would load them all into ChimeraX their sizes are represented correctly, but that’s just too much for the computer.

So, thanks in advance for your help.

Best wishes Christoph Bachmann University Basel - Switzerland

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