General error or specific for my setup?

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Wed Jan 10 04:19:09 EST 1996


In <PMR.96Jan9204201 at unst.sanger.ac.uk> pmr at sanger.ac.uk writes:

> In article <4cu1g5$7bb at rc1.vub.ac.be> palard at dec5 (Philippe Alard) writes:
> >   Christoph Gartmann (GARTMANN at IMMUNBIO.MPG.DE) wrote:
> >   : we have SRS V4.08 under VAX-VMS, the sequences are in GCG format, the GCG
> >   : databases have been created as "novmsonly". Now I do a 
> >   :    getz -d "[SWISSPROT-ID:cra2_mesau]"
> >   : to view the sequence data. Result: the comment line in the GCG .SEQ-file is
> >   : treated as sequence characters and the sequence itself is truncated. 
> >
> >   : Question: does this happen on other sites? Under Unix, VMS-VAX, VMS-AXP,
> >   : with or without "novmsonly"?
> >
> >    Yes we have the same problem under Unix. We also run srs v4.08.
> 
> Just to counter these two sites - we run srs 4.08 on Unix (Irix 5.2)
> and have no problems like this.
> 
> Is this only with "novmsonly" VMS formatting of databases, or is
> this also happening to some pure Unix sites?

I looked a bit deeper into it: it happens independent of the "novmsonly"
switch. It depends on the format of the sequence  - 2BIT or ASCII. With 2BIT
things are fine but with ASCII the error occurs. Example: EM_PAT A00674 (2BIT)
and A00709 (ASCII). But of course, I can only check the VMS version.

Regards,
   Christoph Gartmann


+----------------------------------------------------------------------------+
| Max-Planck-Institut fuer      Phone   : +49-761-5108-465   Fax: -221       |
| Immunbiologie                 PSI     : PSI%(0262)45050160374::GARTMANN    |
| Postfach 1169                 Internet: gartmann at immunbio.mpg.de           |
| D-79011  Freiburg, FRG                                                     |
+----------- Do you know MENUE, the user environment for OpenVMS? -----------+




More information about the Bio-srs mailing list