[Chimera-users] 3D dashed pseudobond styles?

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 6 10:25:32 PST 2015


Hi Oliver,
I agree it would be very handy.  What I do to fake it in Chimera now is just add a distance and then hide the distance label, for example with command:

setattr p label “” sel

(where sel is selected end atoms of the pseudobonds of interest, or you could give an actual atomspec that included all the end atoms of the pseudobonds of interest).  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

Or you could do it using the GUI by selecting all the pseudobonds of interest with Ctrl-click, Shift-Ctrl-click and then in the Selection Inspector, setting the pseudobond label to blank.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

Best,
Elaine

P.S. Regarding Eric’s suggestion, I personally have a hard time getting a good image out of the raytracing option, mainly that it often looks too dark and contrasty, and I find that the 3D dashes can look a lot different than in the Chimera window (e.g. very tiny short dashes), so I tend not to recommend it.   However, you could take a look and see what you think.


On Nov 6, 2015, at 10:06 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> It does indeed Elaine, very much looking forward to trying out Chimera 2!
> 
> Yes, I am aware of the pseudobond reader, and it’s great for scripting or when extensive per bond customization is required, but a single command allowing addition of a pseudo bond between two atoms would be handy in cases when one doesn’t need all the options that are available in the pseudobond reader.
> 
> You know, that would actually also solve the third point - if I could create a single pseudobond easily, then I could associate dummy atoms (using ac mc) with the 3D labels and use pseudobonds as arrows.
> 
> Cheers,
> Oli.




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