VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed Jan 17 2007 - 05:43:06 CST

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.
> >
> >
> >
> >
> > ____________________________________________________________________________________
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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
>