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