VMD-L Mailing List

From: bo baker (bo.bybaker_at_gmail.com)
Date: Fri Aug 31 2007 - 01:55:26 CDT

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.
>
>