VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Feb 01 2011 - 14:19:55 CST

David Guertin wrote:
> Kirby,
>
> Thanks for suggestion. I have installed VMD 1.9, and it behaves the same
> way as 1.8.7: i.e., the filters do not show up in multiseq.
>
> What files are the Domain/Kingdom/Phylum filters read from? I'm
> wondering if there's a simple problem in reading those files.

I've tested it in windows and linux with versions of blast both above and below
the one you are using. I believe that the data you have specifically asked
about is probably downloaded during the metadata file updates that you get the
very first time you run MultiSeq. Are you aware of any problems when MultiSeq
did that initial download? You might try redownloading the data. Move/delete
the directory that the files (lots of megabytes) were put in, and get rid of the
multiseqrc file that was created in your user directory. Then, rerun VMD and
Multiseq and have it redownload everything. This is definitely a problem we
haven't run across before. :)

Kirby

>
> Dave
>
> On 2011-02-01 12:08, Kirby Vandivort wrote:
>> 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