[Chimera-users] 3D dashed pseudobond styles?

Oliver Clarke olibclarke at gmail.com
Fri Nov 6 10:27:27 PST 2015


Thanks for the tips Elaine! Yes, I just tried the ray tracing  and I agree, I *much* prefer Chimera rendering, which is also considerably faster.

Oliver.
> On Nov 6, 2015, at 1:25 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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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