[Chimera-users] loading trajectories with no box line

Eric Pettersen pett at cgl.ucsf.edu
Wed Apr 25 10:38:43 PDT 2012

Hi MIchael,
	I'm not 100% sure what "stay in register" means, but if it means that  
molecules are being "wrapped" across box boundaries then you need to  
use the ptraj "image" command to keep molecules from wrapping across  
box boundaries (Chimera currently has no ability to do this wrapping  
on its own).  If this isn't what "stay in register" means then please  
explain further...


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Apr 24, 2012, at 1:40 PM, Michael F. Bruist wrote:

> Is there a way to load trajectories that do not have box lines?  I  
> have trajectories from which most solvent and ions have been  
> stripped.  They were written with ptraj as amber coordinate files  
> with the "nobox" option.  I cannot get these to stay in register for  
> MD movie.  I do not have this problem for trajectories for which the  
> box line has not been removed.

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