VMD-L Mailing List

From: MW Van der Kamp, School of Chemistry (Marc.VanderKamp_at_bristol.ac.uk)
Date: Tue Oct 03 2006 - 04:29:20 CDT

Hi,

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

Thanks,
Marc

--On 03 October 2006 00:38 -0500 John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> I'm guessing you're using VMD 1.8.4? VMD 1.8.5 fixes a
> bug that could cause this type of problem. (specific to loading
> a sequence of PDB files..)
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Oct 02, 2006 at 05:06:33PM +0100, MW Van der Kamp, School of
> Chemistry wrote:
>> Dear all,
>>
>> I have a problem loading a pdb file into a molecule previously read in
>> as a pdb file using a tcl script. After reading in the first pdb file,
>> the connectivity of atoms is correctly displayed. After loading the
>> second pdb file however, all the display shows in points, so bonds seem
>> to be lost. (I use the standard stick representation.)
>> I haven't experienced this before and the same thing does not happen
>> when I use the 'File>Load data into molecule' option of the VMD Main
>> window. Does anyone know how I can solve this?
>>
>> Thanks,
>> Marc
>>
>> PS Start of my tcl script I load using the TkConsole:
>> mol new C:/TEMP/b3lyp/rc1-b3lyp-1.4.pdb waitfor all
>> mol addfile C:/TEMP/b3lyp/rc1-b3lyp-1.3.pdb waitfor all
>> mol addfile C:/TEMP/b3lyp/rc1-b3lyp-1.2.pdb waitfor all
>> mol addfile C:/TEMP/b3lyp/rc1-b3lyp-1.1.pdb waitfor all
>>
>> (Doesn't matter whether I use 'waitfor all' or not)
>>
>> ---------------------------------------------------
>> Marc van der Kamp, PhD-student
>> School of Chemistry, Research group of Dr. Adrian Mulholland
>> University of Bristol
>> E-mail: Marc.vanderKamp_at_bristol.ac.uk
>>
>
> --
> 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

---------------------------------------------------
Marc van der Kamp, PhD-student
School of Chemistry, Research group of Dr. Adrian Mulholland
University of Bristol
E-mail: Marc.vanderKamp_at_bristol.ac.uk