VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 14 2005 - 09:46:01 CDT

Adrian,
  Whenever you have directories with spaces in them, you need to quote
the directory name to prevent the shell from misinterpreting the name,
the same goes if you were in a command line shell window.

  John

On Thu, Apr 14, 2005 at 07:03:41PM +0800, Adrian Koh wrote:
> Hi,
>
> Thank you very much for your replies. I've added the following lines in
> "vmd.rc" in order to change the default directory:
>
> # change default Home directory
> cd /Nanowire Simulations/
>
> and an error message appeared during startup saying:
>
> wrong # args: should be "cd ?dirName"?
>
> and the default directory remained as what it was previously. Where did
> I go wrong?
>
>
> Regards,
> Adrian.
>
>
>
> Axel Kohlmeyer wrote:
>
> >On Thu, 14 Apr 2005, Adrian Koh wrote:
> >
> >AK> Dear all,
> >
> >dear adrian,
> >
> >AK>
> >AK> I'm trying, with much difficulties, to get through Chapter 12 of the
> >AK> User Manual.
> >AK>
> >AK> I'm attempting to customize VMD to my preferred defaults like a
> >"White" AK> background, "Orthographic" display, "VDW" graphic
> >representation, and AK> setting the default directory to my own directory,
> >in order to avoid the AK> tedious process of redirecting from the VMD
> >directory every time I want AK> to open a file somewhere else.
> >
> >for most of this you need to set up a .vmdrc file in your home
> >directory (or vmd.rc when using windows)
> >
> >so for background, orthographic you can see e.g.:
> >http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part1.html#chap3_sect1
> >
> >setting the 'home' directory can be easily done
> >with adding a 'cd /my/home/directory' in the .vmdrc/vmd.rc file.
> >
> >now setting the default visualization is more tricky. you
> >can of course hack the vmd source code and recompile. but
> >there are also ways of hook into the process of loading
> >a molecule. an example of how to do the latter is at
> >
> >http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect2
> >
> >but note that this is some kind of a hack and will not
> >work under all circumstances and especially pay attention
> >to the warning.
> >
> >AK> Can any one explain simply how could this be done? Thank you very
> >much :).
> >
> >i hope this is simple enough,
> > axel.
> >AK>
> >AK>
> >AK> Regards,
> >AK> Adrian
> >AK>
> >
> >
> >
> 

-- 
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