[Chimera-users] 3D movies for projects

Kenward Vaughan kay_jay at earthlink.net
Sun Jan 29 13:56:22 PST 2017

On 01/29/2017 12:17 PM, Elaine Meng wrote:
> Hi Kenward,
> Just a couple of notes about ChimeraX commands:
> - “view” is the “focus” equivalent
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html>
> - although zones can’t be specified directly in other commands like show or color (yet),  there is a “select zone” to which Tom just added a residues option (for residue-based cutoff, not yet documented) and a “surface zone”
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#zone>
> No hbonds yet, though!
> Best,
> Elaine

Ah, but this is definitely closer to the desired product!  :-)

Are there any commands in place yet to draw in bonds, so it can be 
scripted in to created H-bonds once one knows which atoms are involved? 
(I realize that this may be basic and I should know better, but it's so 
easy just to raise my hand and ask...)


>> On Jan 28, 2017, at 2:25 PM, Kenward Vaughan <kay_jay at earthlink.net> wrote:
>> Thanks for the input, Tom.  I've been playing with ChimeraX now and find that there are features still missing (understandably) which will limit the presentation, such as not having zone selection with extend, hbonds, and something equivalent to focus.
>> While I may be able to come up with their rough equivalents to achieve the desired results, I'm not sure my students would be up to the task. The idea is to make it a bit of a challenge but more importantly to be fun seeing things come together relatively quickly.
>> Back to Chimera itself--can a side-by-side movie be generated which would work in a VR setup?  If so, what sorts of changes might we look for in the settings for the camera (eye separation, screen distance, etc.)??
>> This moves away from the immersion experience but still could easily bring a student's presentation outside to the masses to view...
>> Kenward

In a completely rational society, the best of us would aspire to be
_teachers_ and the rest of us would have to settle for something less,
because passing civilization along from one generation to the next
ought to be the highest honor and the highest responsibility anyone
could have.     - Lee Iacocca

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