VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Oct 03 2006 - 08:07:39 CDT

On Tue, 3 Oct 2006, MW Van der Kamp, School of Chemistry wrote:

MV> Hi,
MV>
MV> You were right, John, thanks a lot. I installed VMD 1.8.5 this morning and
MV> my problem is solved.
MV> By the way, do you (or someone else) know of a trick to load files in a
MV> tcl-script from windows folders with spaces in the name?
MV> With the Windows XP setup that's standard on computers in our department
MV> you get "C:/Documents and Settings/chmwvdk/" folders for each user. Due to
MV> the spaces in the name a normal tcl-script will assume the end of the file
MV> location at the first space of course...

even if you use?

mol new {C:/Documents and Settings/chmwvdk/some file.pdb} type pdb waitfor all

axel.

MV>
MV> Thanks,
MV> Marc
MV>
MV> --On 03 October 2006 00:38 -0500 John Stone <johns_at_ks.uiuc.edu> wrote:
MV>
MV> > Hi,
MV> > I'm guessing you're using VMD 1.8.4? VMD 1.8.5 fixes a
MV> > bug that could cause this type of problem. (specific to loading
MV> > a sequence of PDB files..)
MV> >
MV> > John Stone
MV> > vmd_at_ks.uiuc.edu
MV> >
MV> > On Mon, Oct 02, 2006 at 05:06:33PM +0100, MW Van der Kamp, School of
MV> > Chemistry wrote:
MV> >> Dear all,
MV> >>
MV> >> I have a problem loading a pdb file into a molecule previously read in
MV> >> as a pdb file using a tcl script. After reading in the first pdb file,
MV> >> the connectivity of atoms is correctly displayed. After loading the
MV> >> second pdb file however, all the display shows in points, so bonds seem
MV> >> to be lost. (I use the standard stick representation.)
MV> >> I haven't experienced this before and the same thing does not happen
MV> >> when I use the 'File>Load data into molecule' option of the VMD Main
MV> >> window. Does anyone know how I can solve this?
MV> >>
MV> >> Thanks,
MV> >> Marc
MV> >>
MV> >> PS Start of my tcl script I load using the TkConsole:
MV> >> mol new C:/TEMP/b3lyp/rc1-b3lyp-1.4.pdb waitfor all
MV> >> mol addfile C:/TEMP/b3lyp/rc1-b3lyp-1.3.pdb waitfor all
MV> >> mol addfile C:/TEMP/b3lyp/rc1-b3lyp-1.2.pdb waitfor all
MV> >> mol addfile C:/TEMP/b3lyp/rc1-b3lyp-1.1.pdb waitfor all
MV> >>
MV> >> (Doesn't matter whether I use 'waitfor all' or not)
MV> >>
MV> >> ---------------------------------------------------
MV> >> Marc van der Kamp, PhD-student
MV> >> School of Chemistry, Research group of Dr. Adrian Mulholland
MV> >> University of Bristol
MV> >> E-mail: Marc.vanderKamp_at_bristol.ac.uk
MV> >>
MV> >
MV> > --
MV> > NIH Resource for Macromolecular Modeling and Bioinformatics
MV> > Beckman Institute for Advanced Science and Technology
MV> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
MV> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
MV> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
MV>
MV>
MV>
MV> ---------------------------------------------------
MV> Marc van der Kamp, PhD-student
MV> School of Chemistry, Research group of Dr. Adrian Mulholland
MV> University of Bristol
MV> E-mail: Marc.vanderKamp_at_bristol.ac.uk
MV>
MV> 

-- 
=======================================================================
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.