[Chimera-users] sphere transparency

Thomas Pochapsky pochapsk at brandeis.edu
Mon Jun 12 13:12:05 PDT 2017

Thanks, Elaine,

This works independently (just applying through the per-frame script in 
the movie viewer), but I am trying to integrate it with the morph that I 
generated (120 frames); right now it keeps flashing the structure of the 
ligand as it appears to fade back and forth on each frame of the morph 
(at least that is what it looks like to me).

Here are the script commands I have tried, again in the per-frame 
scripting window accessed from the movie viewer:

transp 100,a #4:MIV1
transp 0,a #4:MIV frames 60
transp 100,a #4:MIV frames 121

Ideally, the substrate-bound form is reached at frame 60 of the morph, 
by the time it reaches 121 it has gone back to the substrate-free form.  
So I would like to have the substrate fade in by frame 60, and back out 
again by 121.

And while we are at it, how would I go about selecting side chains that 
interact with the substrate on the morph model?   If I use *ligand 
zr<5*, Chimera decides that the heme is the ligand, not the :MIV.

Thanks in advance.  Sorry, I am brand-new to this, I just found out that 
PyMOL can't do all the things I need...

Tom Pochapsky

On 6/12/17 1:50 PM, Elaine Meng wrote:
> Hi Tom,
> The broader command is simply “transparency” … it applies to not only surfaces, but also atomic representations, ribbons, etc. (whichever you specify) and there is a “frames” option for fading in/out over a specified number of frames.  So for example with this ligand in 2gbp, the last command would fade it from the initial 0% to 100% transparent over 100 frames:
> open 2gbp
> show :bgc
> repr sphere :bgc
> transp 100,a :bgc  frames 100
> … in this case “ligand” could be used instead of “:bgc” but I showed a more general case of specifying by residue name, since “ligand” doesn’t always get what you want.  The “,a” means to affect atomic representations, not surfaces, ribbons, etc.  See the manpage:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>
> The “surftransparency” manpage (e.g. shown with command “help surftransparency” refers to this “transparency” command which essentially replaces it, although surftransparency still works too.   See also the movie-related commands list, including “coordset” to play through your morph.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
> There is also a list of all commands, of course…
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
> … and you can also use "Help… Search Documentation” in the menu to search for specific terms like “transparency"
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jun 12, 2017, at 10:35 AM, Thomas Pochapsky <pochapsk at brandeis.edu> wrote:
>> Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand?  I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme.  I will probably have other questions, but this seems like a good place to start...
>> Thanks,
>> Tom Pochapsky

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