VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Feb 01 2011 - 11:08:55 CST

David,

Thus far I have been unable to recreate your problem. I've tried on Linux using
the latest beta as well as version 1.8.7, and I'm copying the tutorial files
onto a windows box we have to do some testing there. In the meantime, I would
suggest trying out the latest beta version of VMD. Numerous changes have been
made to MultiSeq, in particular, which might make your experience more enjoyable.

   http://www.ks.uiuc.edu/Research/vmd/alpha/

Thanks,

Kirby

David Guertin wrote:
> I have installed VMD, Multiseq, and BLAST on a Windows XP machine, and
> am testing the installation using the tutorial "Evolution of
> Translation: Class-I Aminoacyl-tRNA Synthetases" at
> http://www.scs.illinois.edu/schulten/tutorials/index.html.
>
> Everything that I have tested is working correctly except for one thing:
> when I import BLAST data in Multiseq, the only filters that I am
> presented with are "All" and "Unknown;" I do not see Archaea, Eukaryota,
> or anything else.
>
> The steps (section 3.4.1 in that tutorial) are as follows:
> 1. In Multiseq, select the 1U7D_A sequence.
> 2. Select File > Import Data.
> 3. Select From BLAST Search.
> 4. Select Marked Sequences.
> 5. Select the TUTORIAL_DIR/swiss-prot/uniprot_sprot database.
> 6. Set E score to e-20 and iterations to 1.
> 7. Select OK to run the search.
>
> That all works as advertised.
>
> But in the results window (Figure 12 in the tutorial document), while
> the reulting 44 sequences are displayed correctly, the Filter Options
> box is empty except for "All" and "Unknown." There is no listing for
> Archaea, Eukaryota, or anything else.
>
> Have I missed something?
>
> This is with VMD 1.8.7 and BLAST 2.2.20 (bundled with the tutorial
> package), running on Windows XP SP3.
>
> I'm hoping someone can help!
>
> Dave Guertin
> 

-- 
Kirby Vandivort                      Theoretical and
Senior Research Programmer            Computational Biophysics
Email: kvandivo_at_ks.uiuc.edu          3061 Beckman Institute
http://www.ks.uiuc.edu/~kvandivo/    University of Illinois
Phone: (217) 244-1928                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA