AMBER Archive (2003)

Subject: Re: Protein Reorientation

From: samantha hughes (s.j.hughes_at_imperial.ac.uk)
Date: Mon Mar 03 2003 - 08:02:11 CST

Hi Gemma

One way to do this would be to calculate the transformation matrix used
to reorient the protein (vmd will do this, search through the manual for
"set transformation_matrix". You can then apply the same transformation
matrix to the original orientation within Leap, using the transform
command.

Hope this helps,
Samantha

On Mon, 2003-03-03 at 13:54, Gemma Kinsella wrote:
> Hi all,
>
> I've come across what should be a trivial problem while trying to set up a
> membranne protein simulation in a bilayer. I wish to reorientate the
> position of my starting protein so it will lie straighter in the bilayer
> during set-up. (i.e. loops at top and bottom)
>
> While I have no problem doing so visually, (weblab viewer, vmd, sybyl) I have
> been unable to find a piece of software that will allow me to save the
> proteins new coordinates to be introduced to leap and was hoping someone
> could point me in the right direction.
>
> Many thanks,
>
> Gemma
>
>