VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 23 2006 - 11:46:13 CST

Francis,
  You can perform arbitrary matrix transformations using
atom selections, with something like this example below,
from the VMD User's Guide:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node177.html#13438

# Rotates the side chain atoms around the CA-CB bond by 10 degrees.

# get the sidechain atoms (CB and onwards)
set sidechain [atomselect top "sidechain residue 22"]
# get the CA coordinates -- could do next two on one line ...
set CA [atomselect top "name CA and residue 22"]
set CAcoord [lindex [$CA get {x y z}] 0]
# and get the CB coordinates
set CB [atomselect top "name CB and residue 22"]
set CBcoord [lindex [$CB get {x y z}] 0]
# apply a transform of 10 degrees about the given bond axis
$sidechain move [trans bond $CAcoord $CBcoord 10 deg]

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 23, 2006 at 08:08:45AM -0700, Francis Reyes wrote:
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> I have been using VMD for a few months mostly just changing
> representations of molecules to show important structural properties.
> However, I'm interested in modifying the structures in VMD. Are there
> any tutorials that can explain how do to manipulations to whole
> domains? e.g. rotate a whole domain around an alpha helix 90 degrees?
>
>
> Thanks
>
> FR
>
> - ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
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-- 
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