VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jun 05 2018 - 07:55:00 CDT

Hi Lorenzo,

The OPM (orientation of proteins in membrane) database is the tool I'd recommend. http://opm.phar.umich.edu/

-Josh

On 2018-06-04 21:35:33-06:00 owner-vmd-l_at_ks.uiuc.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