VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 29 2007 - 16:22:23 CDT

Hi,
  With the pre-1.8.6 versions of VMD using the "AtomSel" module
(VMD 1.8.6 provides a new atom selection module replacing the old one):

   align(ref=None, move=None, frame=None, weight=None): RMSD alignment
    Finds transformation to align atoms in selection with ref,
    using given weight, and applies the transformation to atoms
    in move. If ref is not given, coordinates in frame 0 of the
    selection are used. If move is not given, all atoms in the
    molecule are moved; otherwise, only atoms in move are moved.
    frame can be used to apply the transformation to a different
    timestep than the current one. Note that frame overrides the frame
    in both sel and move. If you want to use different frames for
    sel and move, use sel.frame(i).align(move.frame(j))

Cheers,
  John

On Thu, Mar 29, 2007 at 07:27:21PM +0200, Per Jr. Greisen wrote:
> Hi,
>
> I have made a script where I choose specific residues in a protein and
> would like to align them with each other.
>
> .....
> .....
> .....
> pro_2 = sel.AtomSel('residue 1 or residue 2',nid)
> pro_2.frame(0)
>
> pro_2.align()
>
> which gives me the following error
> AttributeError: 'list' object has no attribute 'align'
>
> so how to fix this? Any help appreciated thanks in advance.
>
> Best Regards
>
> Per
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078