[Chimera-users] sphere transparency

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 12 14:38:13 PDT 2017

> On Jun 12, 2017, at 1:48 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> So it cannot be done within a per-frame script in the playback tool (MD Movie). 

It turns out that “cannot” was a little too strong… I’d forgotten that there is a mechanism in per-frame scripts to only execute a command at a particular trajectory frame, by prefixing it with #N:.  I had an example morph (2fw0 -> 2gbp -> 2fw0) 121 frames where the middle structure has bound BGC, and in that case I could use this per-frame script

#1:trans 0,a :bgc frames 60
#61:trans 100,a :bgc frames 60

However, the other method with “coordset” in a script may still be superior for  at least two reasons:
(1) If you use the per-frame script method above, you also have to move the MD Movie slider to the far right to ensure a 1-to-1 relationship between trajectory frames and image update frames.  If you have the slider somewhat to the left there will be more than one image update frame per trajectory frame and the fade-in and fade-out over 60 frames will occupy a smaller fraction of the trajectory.  Yes, you could increase the transparency command frames number from 60 to something bigger, but hard to tell exactly how much bigger to make it.

(2) The “coordset” command method has more control.  You could choose to insert a pause between the two stages of the morph, for example to linger on the bound state for a while before starting the fade-out and morph to unbound state:

trans 100,a :miv
coordset #5 1,60; trans 0,a :miv frames 60; wait 60
wait 20
coordset #5 61,121; trans 100,a :miv frames 60; wait 60

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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