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RE: problem with sequence search



Hi,

As a remainder to everybody: 6v0 has CHAINS files corrupted, therefore
if you are using SEQUENCE_SEARCH you will need to install 6v1. You can
download it from the MODELLER web site at:
http://salilab.org/modeller

Thanks,
Bozidar



-----Original Message-----
From: 
[">mailto:] On Behalf Of
michael hanlon (BITS)
Sent: Tuesday, April 09, 2002 11:19 AM
To: ''
Subject: problem with sequence search


I'm running v6 on ReDHat 7.2 on a PIII.
I tried the following script for a sequence search:

SET OUTPUT_CONTROL = 1 1 1 1 0
SET SEARCH_RANDOMIZATIONS = 20
SET SEARCH_CHAINS_LIST = '${MODINSTALL6v0}/modlib/CHAINS_3.0_40_XN.cod'
SEQUENCE_SEARCH FILE = './TvLDH.ali', ALIGN_CODES = 'TvLDH' DATA_FILE =
ON

but get the following error, the last bit of which seems to indicate
that 1xnb cannot be found, and yet it's there alright:

TOP_________>     2    2 SET SEARCH_RANDOMIZATIONS = 20
TOP_________>     3    3 SET SEARCH_CHAINS_LIST =
'${MODINSTALL6v0}/modlib/CHAINS_;                       3.0_40_XN.cod'
TOP_________>     4    4 SEQUENCE_SEARCH FILE = './TvLDH.ali',
ALIGN_CODES =
'TvLD;                       H'
openf5__224_> Open       11  OLD  SEQUENTIAL
${MODINSTALL6v0}/modlib/CHAINS_3.0_40_XN.cod
openf5__224_> Open       11  OLD  SEQUENTIAL
${MODINSTALL6v0}/modlib/CHAINS_3.0_40_XN.cod
openf5__224_> Open       11  OLD  SEQUENTIAL
{MODINSTALL6v0}/modlib//CHAINS_all.seq
read_se_367E> Sequence not found; code:  P1;1xnb
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Any ideas?

Mike

Dr. Mike Hanlon
Molecular Biology Computing Support
BBSRC Bioscience IT Services
West Common
Harpenden
Herts AL5 2JE 
Phone: 01582 714904
Email: 
Web: http://www.molbiol.bbsrc.ac.uk