[Chimera-users] bond transparency as a function of length?
pett at cgl.ucsf.edu
Mon Jun 4 14:10:27 PDT 2012
Great! Glad your got it to work and kind of impressed you resolved
those issues on your own! I'm envisioning a lot of nosing around the
Chimera code on your part to see how the sausage is made. :-)
On Jun 4, 2012, at 9:50 AM, Kersey Black wrote:
> Hi Eric,
> Thanks so much for the help. I was able to quickly get the basic
> I wanted, and I would not have gotten there without your guidance.
> In the process
> I ran into a few small issues that come simply from not yet
> understanding the overall
> structure of the data and its representation, and its interaction in
> the python interface.
> But that is coming together. Notably, I needed to find other ways
> to select the
> bonds that would have be affected by the fading and also how to
> control element colors
> in the context of applying this to C-C bonds in a simple
> hydrocarbon. Evidentially, an arbitrary color
> gets applied to the model as a whole when it comes up, and then when
> fading the bonds
> they would sometimes fade to reveal that underlying solid color.
> But I have sorted those things out.
> The Python interface is very cool.
> Thanks again.
> On May 29, 2012, at 3:08 PM, Eric Pettersen wrote:
>> On May 29, 2012, at 12:29 PM, Kersey Black wrote:
>>> 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
>>> here I am lost. Any hints, links or suggestions would be very much
>> 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
>> 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
>> 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
>> 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 Pettersen
>> UCSF Computer Graphics Lab
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