[Chimera-users] bond transparency as a function of length?

[Eric Pettersen]

On May 29, 2012, at 12:29 PM, Kersey Black wrote:

> Hi,
>
> Very recent to Chimera.  Trying to set the transparency of a bond
> to be a function of bond length in each frame of a trajectory.
> I have figured out how to define a transparent color, and
> now I am imaging the solution might use something like range color
> to vary the blending of the opaque version of the color and the
> fully transparent version based on distance, with the distance being
> determined as a per frame attribute of those atoms, but someplace  
> around
> here I am lost.  Any hints, links or suggestions would be very much
> appreciated.

Hi Kersey,
	This is doable but you have to resort to Python, and even then it's  
tricky.  The issues are:

1) By default, bonds are colored in "halfbond" mode, where each half  
of the bond is colored the same as the corresponding endpoint atom.
2) There is no command to set only the transparency of a bond.  There  
is a 'bondcolor' command which sets the red, green, and blue  
components as well (and also takes the bond out of halfbond mode).   
The 'transparency' command works on atoms, not bonds (but bonds in  
halfbond mode "inherit" the transparency changes of their endpoint  
atoms).
3) In Python, changing the transparency component of a color object  
will affect every atom/bond/molecule using that color object, so the  
bonds you want to vary the transparency of will have to have unique  
color objects assigned to them.

	So, as best I can determine the general plan of action would be:

1) Select the bond or bonds you want to do this for using whatever  
means you like.
2) Store a list of the selected bonds in the Python layer and create  
color objects for them.
3) Each frame, assign distance-dependent transparency values

You do both steps 2 and 3 with Python scripts in the Per-Frame dialog  
of the MD Movie tool.  For step 2 you input the script, click Apply  
and execute 1 step of your trajectory.  Then back up the trajectory  
and input the script for step 3, click OK, and run the trajectory.   
Here are the scripts:

(step 2)
bonds = mdInfo['mol'].ghostBonds = chimera.selection.currentBonds()
for b in bonds:
         b.halfbond = False
         b.color = chimera.MaterialColor(*b.molecule.color.rgba())


(step 3)
for b in mdInfo['mol'].ghostBonds:
         dist = b.length()
         if dist <= 2.0:
                 opacity = 1.0
         elif dist >= 5.0:
                 opacity = 0.0
         else:
                 opacity = 1.0 - (dist - 2.0) / 3.0
         b.color.opacity = opacity

For the step 3 script, change the distance cutoff values and  
interpolation formula as you like to fit your needs.  I've attached  
the scripts as files so that you can save some typing and use the  
'insert from file' button on the Per-Frame dialog.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

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