VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 31 2007 - 02:08:30 CDT

Hi,
  If you want to align visually, rather than by text commands you can use the
Mouse->Move->... menu items (atom, residue, fragment, molecule, etc).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 31, 2007 at 04:25:26PM +0930, bo baker wrote:
> Hi, Axel:
>
> I followed the examples from "Membrane Plugin" and tutorial "Explicit
> Membrane Protein Simulations in NAMD/VMD". None of them mentioned
> transformation matrices. Instead, it says: aligning can be easily done
> using the VMD GUI front end. Then save the protein coordinates in
> another PDB file.
>
> Thanks
>
> Bo
>
> On 8/31/07, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
> > On Fri, 31 Aug 2007, bo baker wrote:
> >
> > hello bo,
> >
> > please check the mailing list archives. VMD does not
> > change the coordinates with your operations, but rather
> > changes the view on them. you have to change coordinates
> > by applying transformation matrices. this has been discussed
> > before for a similar example.
> >
> > cheers,
> > axel.
> >
> > BB> Hello, VMD:
> > BB>
> > BB> I try to merge my protein with membrane using VMD. Here is how I did:
> > BB>
> > BB> load meambrane files (psf and pdb)
> > BB> load protein files (psf and pdb)
> > BB>
> > BB> Fix membrane
> > BB> move and rotate protein to the position where I wanted (top of the membrane)
> > BB> save protein coordinate in another PDB file (with selecting "all")
> > BB>
> > BB> The new PDB file moves to a paralled (compared with the original one)
> > BB> new position, but not the position where I aligned it with the
> > BB> membrane. I tried several times. The new PDBs are in new positions but
> > BB> paralled to the original one, not on the top of the membrane.
> > BB>
> > BB> I don't know if I did something wrong.
> > BB>
> > BB> I tried on VMD 1.8.2 and VMD 1.8.6.
> > BB>
> > BB> Thank you for your help
> > BB>
> > BB> Bo
> > BB>
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> >
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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