[EMBOSS] Configuring EMBOSS to use getz

Ran Rubinstein ranrub at md.huji.ac.il
Wed Oct 8 15:50:28 UTC 2003

Your dbalias parameter is probably wrong. It should be the name of the
databank in SRS. Try to run getz directly with your query and see whether it

Ran Rubinstein 
Dept. of Molecular Biology 
Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel
Tel +972-2-6757906 Fax +972-2-6758992

-----Original Message-----
From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk] On
Behalf Of yann-francois.bizouerne at bayercropscience.com
Sent: Wednesday, October 08, 2003 5:33 PM
To: emboss at embnet.org
Subject: [EMBOSS] Configuring EMBOSS to use getz


I am trying to use the method "srs".
I am using Emboss  2.7.1 and SRS 7.1.

In my emboss.default file, I have :

   DB Nrl3dGetz [
   methodquery: srs
   format: pir
   type: P
   comment: "NRL 3D using SRS"
   app: getz
   methodall: direct
   file: "*.seq"
   dir: $emboss_data_dir/nrl_3d

When I execute the command "showdb", I obtain :

   Displays information on the currently available databases
   # Name        Type ID  Qry All Comment
   # ====        ==== ==  === === =======
   Nrl3dGetz     P    OK  OK  OK  NRL 3D using SRS

So I looks fine. But when I try to find an entry, I just obtain a error.

   user>entret Nrl3dGetz:11ASA -outfile stdout
   Reads and writes (returns) flatfile entries
   error: Unknown set or databank
     No set or library named "Nrl3dGetz"
   Error: Unable to read sequence 'Nrl3dGetz:11ASA'
   Died: entret terminated: Bad value for '-sequence' and no prompt

I have read all the SRS and EMBOSS documentations  related to this
and I don't know where the problem is.
Do you have any clue ??

Thanks in advance.

Yann-François BIZOUERNE
BioInformatic Team
BAYER CropScience
1, rue Pierre Fontaine
91058 Evry Cedex
Phone:      33-(0) 1-69-47-61-56
FAX:        33-(0) 1-69-47-61-42
E-mail:     yann-francois.bizouerne at bayercropscience.com
Intranet: http://bioinfo.evry.fr.bayercropscience/

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