VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 17 2007 - 12:26:48 CST

Hi,
  The built-in PSF plugin for VMD is mainly used as a reader, as VMD
doesn't store enough information internally to maintain 100% of the PSF
content when a new one is written out again. If you want to edit the structure
and emit a new PSF with complete information, you'll need to regenerate it
using autopsf, or by calling psfgen with your own script. Future revs of
VMD will add the necessary interfaces and storage so that all of the
information stored in a PSF can be preserved for ease of modification.
For now, the best thing is to write out the new PDB and then use
autopsf or psfgen to regenerate the PSF from that and the appropriate
topology/parameter file(s).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 17, 2007 at 12:43:06PM +0100, Himanshu Khandelia wrote:
> Hi,
>
> I am new to the VMD text interface, and am facing a little problem.
>
> I am
> 1. reading in a pdb, psf pair into vmd
>
> 2. moving around a few things, and
>
> 3. writing out a new pdb-psf pair.
>
> Although the pdb is written out correctly, the psf is not. Specifically,
> the 5th and 6th columns in the psf are both the atom names. While in a
> correct psf, the 6th column should be atom-type. The problem might be
> that I am not reading the original psf correctly in the first place. I
> have described the problem in a little more detail below :
>
> Example script:
>
>
>
>
>
>
> ----------------------------
> Himanshu Khandelia
> Research Assistant Professor (Postdoc)
> MEMPHYS, Center for Membrane Physics
> University of Southern Denmark (SDU)
> Odense M 5230, Denmark
> www.memphys.sdu.dk
> Phone: +4565503510
> email: hkhandel_at_memphys.sdu.dk
> -----------------------------
>
>
>
> On Wed, 17 Jan 2007, John Stone wrote:
>
> >
> > Hi,
> > You can edit the VMD startup script so it doesn't run the process
> > in a new xterm, and instead runs it within the existing shell/window
> > you ran it from. Have a look at the lines that test for the DISPLAY
> > environment variable towards the end of the 'vmd' script and you'll
> > see what I mean. The main things the startup script does are set
> > the default window position and size, and several environment variables
> > VMD uses to find it's installation location. Windows and MacOS X versions
> > of VMD do this using different techniques. They query the system
> > registry or use other system variables to find the installation location.
> > For the Unix versions of VMD, you can modify the VMD startup script
> > any way you like. In our lab for example, the VMD startup script we
> > use consults a master configuration file which sets the default window
> > position and size differently for different workstations depending on
> > their video hardware configuration, whether or not they have a
> > Spaceball or other 3-D input device, and so on. Let me know if you
> > need more assistance with modifying your VMD startup script.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Jan 16, 2007 at 10:33:27PM -0800, Rob wrote:
> > >
> > > Hi,
> > >
> > > I'm using vmd 1.8.5 on Linux.
> > > When I call vmd, it opens the usual three windows
> > > (display, main and console) and then immediately
> > > forks itself into the background. Is there a way to
> > > disable this and keep vmd running in the foreground?
> > >
> > > Thanks,
> > > Rob.
> > >
> > >
> > >
> > >
> > > ____________________________________________________________________________________
> > > Be a PS3 game guru.
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> >
> > --
> > 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