VMD-L Mailing List

From: David Guertin (guertin_at_middlebury.edu)
Date: Tue Feb 01 2011 - 10:49:24 CST

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 

-- 
David Guertin
Library and Information Services
Voter Hall
Middlebury College
Middlebury, VT 05753