[Chimera-users] mysteries

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 10 16:01:45 PDT 2017

Hi Arthur,
I really can’t tell what you did.  There isn’t an “undo” so I recommend saving a session every now in then if you have done a lot of things. It sounds like maybe some clipping got activated, but as far as I know that wouldn’t get turned on by a simple click in the graphics window.  Maybe you accidentally chose menu: Actions… Focus, which would zoom in and clip to show mostly only the selected stuff.

Regardless of cause, you could try turning off  clipping (command “clip off” or uncheck the box next to “Clip” in the Side View).  If you had carefully adjusted the clipping beforehand, however, that would lose your adjustments.


Another way to rescue the view to see everything, but that may change the zoom and translational position of the scene (up/down, right/left but not rotation) are “View All” button on the Side View or command “focus” or “window” (without options, just the single-word commands).

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

> On Apr 10, 2017, at 3:35 PM, Arthur Szabo <agszabo at outlook.com> wrote:
> After several different occurrences at different times of the same thing I finally decided to ask 1) What happened ?2) How can I reverse it?
> Now the hard part is  to try to described what happened.  I was working on a figure – it  does not seem to depend on its complexity.
> I had a figure on the screen, ribbons colored, selected amino acids visualized.
> I did something with the mouse I believe, though  it might have been that my finger touched something  on the keypad – what  happened was  that the majority of the structure disappeared. Parts of it were there.  I could rotate  it and different parts  of the structure would come into view and what had just been visible faded away. It was like  on rotation portions of the structure would be moving in the plane  of the view, but could move out of that plane  I was also able to enlarge whatever portion of the image was on the screen.
> I know that this is difficult to answer because one really has  to see the result  of whatever I  clicked or something else.  It is not just a random event.
> Thanks for any tips. 
> Arthur G Szabo

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