[Chimera-users] 3D movies for projects

Elaine Meng meng at cgl.ucsf.edu
Sun Jan 29 14:16:24 PST 2017

No problem, I actually had to think about this… there's not yet a ChimeraX command to create pseudobonds, but you can list pairs of atoms in a text file, name it something.pb and then open the file.  Maybe that is still too inconvenient, however.

For example, in ChimeraX "open 1bna" and then the attached text file (if name ends in .pb).  Actually mmCIF of nucleic acids already have the base-pairing H-bonds, as you can see before opening the pb file.  You can control number of dashes with ChimeraX command “style” and color using “color” with “target p” … I don’t think there’s a command for pseudobond thickness yet, however.


I hope this helps,

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> On Jan 29, 2017, at 1:56 PM, Kenward Vaughan <kay_jay at earthlink.net> wrote:
> 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...)
> Kenward
>>> 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
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