srs 5.0 - srscheck

Martin Hilbers mph at dl.ac.uk
Thu Dec 12 09:51:49 EST 1996


Hello folks,

I noted a few odd things with srscheck in the new SRS 5.0

If a library is up to date, it still puts a line like
srsbuild PIR -f '' -xdir 'SRSINX:' -odir 'SRSINX:' -env 'unix'
in the srsupdate file, which gives an error message when you
run it.

Sometimes commands for the compression (and merging) of 
up to date databases are inserted. As far as I could find
out this occurs if one or more of its indices contain 0 entries.

The fssp database at our site consists of a directory filled
with symbolic links to the real fssp data, and the "suppos" and
"comp3D" alternative fssp data. It indexes allright, but srscheck
keeps on thinking that there are 0 entries in that directory,
and orders a reindexing since the index contains 1090 entries.

Another thing which causes some problems is that for single entry
databases getz apparently expects entries to be in a file called
"id.ext" ("id" the id of the entry, and "ext" the extension for the
files in this database.) This works nice if you have a your pdb files
named this way (e.g. 1azu.pdb), but at our site we have names like
"pdb1azu.ent". Indexing goes fine, but retrieving the data is
impossible. A similar problem exists with fssp, were a filename
may have an additional character indicating a different chain.



For the curious people - the experimental (and very much incomplete)
SEQNET srs5.0 server can be found at http://www.seqnet.dl.ac.uk/srs5.0
- but don't  expect things to work there yet.....
Until we have all the icarus files sorted out for all the databases
we have on our srs4 server (http://www.seqnet.dl.ac.uk/srs/srsc) we
will not switch to srs5.


Cheers,

Martin
-- 
-----------------------------------------------------------------
| Martin Hilbers        |    E-mail: m.p.hilbers at dl.ac.uk       |
| SEQNET                |    Tel:    +44-1925-603492            |
| Daresbury Laboratory  |    Fax:    +44-1925-603100            |
| Daresbury, Warrington |---------------------------------------|
| Cheshire WA4 4AD      | SEQNET is the UK national EMBNet node |
| United Kingdom        | http://www.dl.ac.uk/SEQNET/home.html  |
-----------------------------------------------------------------




More information about the Bio-srs mailing list