From: bo baker (bo.bybaker_at_gmail.com)
Date: Sun Sep 02 2007 - 20:18:13 CDT

Hi, John:

It works this time. Thank you very much!

Cheers

Bo

On 9/2/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> How did you attempt to save the coordinates? Did you select a molecule
> in the main VMD form, and then use File->Save Coordinates?
>
> Cheers,
> John
>
> On Sun, Sep 02, 2007 at 09:19:57AM +0930, bo baker wrote:
> > 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
> > >
>
> --
> 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
>