Re: Protein Reorientation

From: Carlos Simmerling <>
Date: Mon, 3 Mar 2003 10:39:19 -0500

If you use my program MOIL-View, you can
save the modified coordinates (including the
rotation) to pdb format for use in leap.
Keep in mind that Leap can also reorient
the molecule (for example, using alignaxes).

moil-view is on the AMBER distribution CD and
also can be found at

----- Original Message -----
From: "Gemma Kinsella" <>
To: <>
Cc: "Gemma Kinsella" <>
Sent: Monday, March 03, 2003 8:54 AM
Subject: Protein Reorientation

> 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
> 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
Received on Mon Mar 03 2003 - 15:53:01 PST
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