[Chimera-users] chimera help in spacing out two structures within the same session

[Elaine Meng]

Dear Kei Onn LAI|,
You can move any models separately from the others with “move” (translate) and “turn” (rotate) commands using their “models” option. You can save positions with “savepos” and you might want to do that before you move the models separately. 

For example:
savepos together
move x 20 mod #1
move x -10 mod #0
savepos apart
reset together
reset apart

The positions are saved in session files.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html>

You can also move individual models by hand if you freeze the others by “deactivating” them (uncheck “A”ctive button in model panel, for example), 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
but usally for figures I prefer the more precise command method so that I don’t accidentally rotate when I want to translate only.

There is also a tutorial where the 2 proteins in an interface are moved apart and rotated like opening a book, 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
but in this case where you are showing crosslinks, it might be better to illustrate them with translation only.  However, you can try different things and see what works for your figure.

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 20, 2019, at 11:44 PM, #LAI KEI ONN# <KEIONN001 at e.ntu.edu.sg> wrote:
> 
> Dear Chimera team
> would appreciate if you have any advice in spacing out two/or more structures within the same chimera session (e.g. the green structure away from the beige ones) so as to clearly visualise the intercrosslinks (red and blue sticks) between two different structures.
> Currently everything is superimposed with one another and i tried separating all the structures into different sessions and recombining it again but it didnt work.
> I am using xlinkanalyzer plugin with chimera.
> Would appreciate your kind advice,
> <image.png>
> 
> thank you!
> Best Regards
> Kei Onn LAI|黎啟諳
> Phd Student
> Lee Kong Chian School of Medicine