From: bo baker (bo.bybaker_at_gmail.com)
Date: Sat Sep 01 2007 - 18:49:57 CDT

Yes, I did move the protein by using Mouse->Move->... menu items. But
can't get the new corrdinate saved as they are shown on the screen.

I am very confused.

Thanks

Bo

On 8/31/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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
> 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
>