VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Jun 04 2018 - 23:29:51 CDT

Question: Membranes are mostly symmetric. Are you sure you want to flip the
protein inside the membrane? Perhaps you want to flip your entire system?

On Jun 5, 2018 15:10, "Lorenzo Casalino" <lcasalino_at_ucsd.edu> wrote:

> Dear VMD users,
>
> I have a protein embedded in a membrane which is upside down and I would
> like to flip it, possibly around its geometrical center, such that it
> assumes its correct orientation.
> Importantly, the first, second and third principal axes of this protein
> are not aligned to the x,y,z axes and I don’t want them to be aligned.
>
> Do you have any suggestion for doing this?
>
> I have tried to play around with the orient package but I was only able to
> do this operation while also aligning the principal axes to the x,y,z axes
> (which I don’t want), using this:
>
> package require Orient
> namespace import Orient::orient
>
> set sel [atomselect top "all"]
> set I [draw principalaxes $sel]
> set A [orient $sel [lindex $I 2] {0 0 -1}]
> $sel move $A
> set I [draw principalaxes $sel]
> set A [orient $sel [lindex $I 1] {0 -1 0}]
> $sel move $A
> set I [draw principalaxes $sel]
>
> Thank you,
> Best regards
>
> Lorenzo
>
>
>