Hello Andrew.
It sounds like you have had great patience with MODELLER - I think you might have actually got the code working properly. The problem could be here :
> SET SEARCH_RANDOMIZATIONS = 100
>From the looks of the manual page concerning the SEQUENCE_SEARCH procedure: http://salilab.org/modeller/manual/node105.html it seems this variable defines the number of repeated, randomised alignments are made in order to get good confidence estimates for your alignments. I would expect modeller will try to do the alignment set 100 times, shuffling your query sequence each time. 100 might be a little bit excessive for a full database search. As for making the 'maximum job time' longer, I've no idea but there is probably another variable for that!
I hope this relieves some of the perplexity. Jim _______________________________________________________________________ Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics Hamburg http://www.zbh.uni-hamburg.de/mitarbeiter/procter