VMD-L Mailing List

From: David Guertin (guertin_at_middlebury.edu)
Date: Tue Feb 01 2011 - 12:50:04 CST

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.

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
>>
>
>