[Chimera-users] help for make figures

Elaine Meng meng at cgl.ucsf.edu
Sat Jul 30 08:55:10 PDT 2016


Hi Liuqing Chen,
In the figure you sent, the part of the ribbon that is highlighted is non-transparent and the rest of the ribbon is partly transparent.  For example, if you have already selected the part you want to highlight, then you could invert selection and set transparency of the non-highlighted part, commands something like:

sel invert
transparency 80 sel
~sel

You would probably want to turn off depth-cueing because that also gives a dimming effect, e.g. command:

~set depthcue

There are different paths to the same result, such as specifying residues directly instead of using a selection:

transp 80 #0:45-188.A

Of course you can use a different number than 80, or only make ribbons (not atoms) transparent, or only surface, etc. Details in the manual.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 30, 2016, at 12:31 AM, 陈柳青 <519198561 at 163.com> wrote:

> HI
> How to make the figures in attachment, which highlight part of a structure.
> Thanks very much for advise. 
> --
> Liuqing Chen
> School of Life Science & Biotechnology
> Minhang Campus
> Shanghai Jiao Tong University 
> No. 800 Dongchuan Road
> Shanghai 200240
> P.R. China
> Tel: +86 21 34207247
> 
> <捕获.PNG>



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