[Chimera-users] transparent ring fill, color by attribute

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 3 16:34:57 PDT 2009

On Aug 3, 2009, at 2:29 PM, Alexey V. Cherepanov wrote:

> Dear Elaine,
> I have another question. On the structure, I color the atoms  
> according to
> their attribute (in my case the chemical shift differences between the
> solution and the solid state NMR). I show the residues as balls &  
> sticks and
> fill the rings of riboses & bases. Can I show the filling (i)
> semitransparent, and (ii) that it keeps the colors of the atoms  
> (e.g. if C1'
> is blue, C2' is white and C3' is red in the ribose ring, then the  
> filling
> should be blue close to C1, white close to C2' and red close to C3'  
> with the
> gradient in between)?
> Many thanks in advance.
> Warm regards,
> Alexey

Dear Alexey,
   The answer to your question is mostly yes, except the color in the  
fill is not smoothly blended.  Currently it shows a "pie slice" or  
wedge for each ring atom.   Some tricky things: (1) the ring fill  
automatically matches the ring atoms, so that you cannot make the fill  
transparent unless the atoms are also transparent.  However, you can  
get around that problem by opening another copy of the same structure  
in which the atoms/bonds are opaque. (2) the transparent ring fill  
must not be thick.  Either it must be in the "thin" style, or if in  
the "thick" style, the atoms and bonds in that copy must be in the  
wire representation (which forces it to really be thin).  Why?   
Because some mysterious extra bonds become visible through the  
transparent fill when it is thick.

- open your structure twice
- assign your attribute (e.g. use bfactor column, or Add Charge, or  
Define Attribute to read your own arbitrary attribute values)
--- for my example, I opened 6bna twice and will use bfactor --
- use one model to make the transparent rings and the other for  
whatever atom/bond display you want
--- I used commands: delete solvent; rep stick --
- start Render by Attribute, move the color bars as you like; for  
each, click the square color well, and in the Color Editor turn on  
"Opacity" and adjust the "A" row (transparency).  There is a "Keep  
opaque" option, and keep that turned on and only click Apply to test  
the coloring.  When the coloring is how you like it, then in the  
"Models" list at the top of the dialog, only choose one of the models.  
Now do not move the coloring bars, only uncheck "Keep opaque" and  
click Apply again.  You won't be able to see any change, but now the  
two models are colored the same except one has the transparency and  
the other does not.
--- I made #0 my transparent model and #1 opaque.  I colored blue->red- 
 >yellow for increasing bfactor.
- now, add thin ring fill to the transparent model, command:  fill  
thin #0

Here is the documentation for the fillring command. Today it is only  
at my site (tomorrow it should show up on the "real" Chimera web site).

The fillring command (or "fill" for short) is brand new and a couple  
things still need fixing:
- to turn off filling, use ~fill ("fill off" and "fill unfilled" are  
not working today)
- saving a session with ring fill should be available in the next  
daily build

Here is a picture of the result:
-------------- next part --------------
A non-text attachment was scrubbed...
Name: thinfill.png
Type: image/png
Size: 153309 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090803/1e8c32f7/attachment.png>
-------------- next part --------------

More information about the Chimera-users mailing list