From: RODRIGOL@BIOMED.UIO.NO (Rodrigo Lopez)
Newsgroups: bit.listserv.info-gcg
Subject: Re:      Re: Longstanding GCG problem
Date: 21 Aug 92 11:52:04 GMT
Organization: The Norwegian EMBnet Node
X-News-Reader: VMS NEWS 1.22

In <01GNSVCQHJCY0004CK@BIOMED.MED.YALE.EDU> Lynna writes:

> >Dear GCG-ers:
> >
> >       We have a problem with our GCG package which we have been unable to
> >solve.  It appears to have to do with the logical names which point to the
> >libraries.  If anyone could guide me as to even where to look first for the
> >errors, I would be MOST appreciative.  Thank you!
> >
> >                                               David Caldwell.
> >
> >Included is a log file demonstrating the error...
> >----------------------------------------------------------------------------
> >$FASTA
> >
> >FASTA does a Pearson and Lipman search for similarity between a
> >
> >query sequence and any group of sequences.  FASTA answers the
> >
> >question, "What sequences in the database are similar to my sequence?"
> >
> >The relationship between FASTA and WORDSEARCH has not been
> >
> >characterized, but FASTA is faster and, for some searches, more
> >
> >sensitive.
> >
> >
> > FASTA with what query sequence ?
> >[cavallius]wendy.pep
> >
> >                  Begin (* 1 *) ?
> >
> >                End (*    37 *) ?
> >
> >
> > Search for query in what sequence(s) (* SwissProt:* *) ?
> >genbank:*
> >
> > What word size (* 2 *) ?
> >
> >
> > List how many best scores and alignments (* 40 *) ?
> >
> >
> > What should I call the output file (* Wendy.Fasta *) ?
> >[cavallius]wendy.fasta
> >
> > *** No sequences to compare to query sequence! ***
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>      EITHER YOUR DATABASE FILES ARE CORRUPT OR YOUR DATABASE LOGICAL IS WRONG!
>      SEE BELOW
> 
> 
> >Image data (records not beginning with "$") ignored
> >$EXIT
> >  CAVALLIUS    job terminated at  6-JUL-1992 13:22:13.86
> >
> >
> 
> David,
>         You have one of two problems; 1) your GenBank database files are
> corrupt or 2) your GenBank logical is not pointing at your GenBank database
> files correctly.
> 
> You can check the directory GenBankDir to see if it has the appropriate files.
> A clue that you may have a bad file would be if it had a different date then all
> the rest of the files in that directory.
> 
> You can check what the logical name GenBank points to on your system.
> You can issue the command $ SHOW LOG GENBANK then check every logical name and
> file that this original GenBank logical points to. Look at the installation and
> maintenance sections of the GCG System Support manual for help in understanding
> the appropriate use of GenBank and other GCG logical names.
> 
>         Tracking down logical and symbol definition problems are some of the
> harder things to do as a GCG system manager. They tend to take a great deal of
> time and patience. The GCG technical support staff have been a great help to me
> in the past with these kinds of problems even thou ultimately it was my own
> stupidity of reassigning the key logical names or symbols. If you feel you are
> getting nowhere fast in finding your problem try calling the GCG technical
> staff.
> 
> Please let us know how you resolve this problem.
> 
> =======================================================================
> - Lynna Stone-Infeld, Manager, Molecular Biology Computing Resources
>                           Internet:  STONE@BIOMED.MED.YALE.EDU
>                                   Bitnet: STONE@YALEMED
> Biomedical Computing Unit, Yale University, School of Medicine
> P.O. Box 3333, New Haven, CT, 06510
> Disclaimer: my opinions are my own and may not be shared by my employer
> =======================================================================
Instead of looking at the GenBankDir directory, try looking at SwissProtDir
which is where the problem report stems from. 

If you are running version 7.x of the GCG programs have a look at your .farm
files making sure the appropiate logicals for accessing the swissprot database
are there. Also, make sure the following logicals are defined: 'sw:', 
'swiss:', and 'swissprot:'

If you do a 'show log sw*' you should get:

        
(LNM$PROCESS_TABLE)

  "SW" = "SWISSPROTDIR:SWISSPROT"
  "SWISS" = "SWISSPROTDIR:SWISSPROT"
  "SWISSPROT" = "SWISSPROTDIR:SWISSPROT"
  "SWISSPROTDIR" = "GENSWISSPROTDISK:[GCGSWISSPROT]"


Another reason for not being able to use the SwissProt Databadse may be a
missing Swissprot.Header file. Make sure there is such a file present in
the swissprotdir. This file should look like this:


NAME: SwissProtDir:SwissProt LN: SWISSPROT SN: SW REL: 22.0 RELDATE: 7/92 FORDAT
E: 7/92 TYPE: P FORMAT: GCG

NOTE!!!! THIS IS A ONE LINE FILE, NOT TWO AS SHOW ABOVE.


A third thing to take into consideration is the current name format of Swissprot
which changed. Previously swissprot entry names had a '$' as separator. Today
this has been replaced for an '_' (underscore character).



Hope this helps a bit...

Rodrigo:-)
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU