VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Aug 31 2007 - 00:17:25 CDT

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
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If you make something idiot-proof, the universe creates a better idiot.