VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Mon Jun 04 2018 - 23:39:24 CDT

Why not do it by hand? Make a graphical representation of just the protein, hit “9” (for move rep), and then grab it with the mouse and rotate (right and center mouse buttons I think?).

Best,
JC

> On Jun 4, 2018, at 10:38 PM, 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
>
>