[chimerax-users] Transparency and Scaling factor in ChimeraX

[Tom Goddard]

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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