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: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of michael hanlon (BITS) Sent: Tuesday, April 09, 2002 11:19 AM To: 'modeller_usage@salilab.org' 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: molbio.support@bbsrc.ac.uk Web: http://www.molbiol.bbsrc.ac.uk