SEQUENCE_SEARCH problems

[Alex Brown <abrown@nimr.mrc.ac.uk>]

Hi.

I recently downloaded and installed MODELLER 6v2 onto a Macintosh 
PowerBook G4 under OS X and Darwin. The installation was successful and 
running the tutorial from the manual (section 1.8.2) produced a result.
I am now having a look at the examples provided by the manuscripts on 
the User Manual page of the Modeller web-site. At this point, I must 
point out that I have been unable to download the example files - I keep 
getting a connection failure error.
I have started by going through the TvLDH (Trichomonas vaginalis lactate 
dehydrogenase) example. I created the file 'TvLDH.ali' as shown in the 
manuscipt, and created the seq_search.top file aslo as detailed :
SET SEARCH_RANDOMIZATIONS = 100
SEQUENCE_SEARCH FILE = 'TvLDH.ali', ALIGN_CODES = 'TvLDH', DATA_FILE = ON

I run this by 'mod seq_search.top'. However, the program appears just to 
sit there not doing much - 30 to 40 minutes so far, before I have to 
quit by Ctrl-C. A .log file is produced, but only contains the 
introductory title and execution start time. is this normal behaviour. 
Changing the SEARCH_RANDOMIZATIONS to 20 appears to have no effect.
As a supplementary question, does anyone know where I could download the 
PDB (or even the ExPDB) database - sequences only, in a FASTA or BLAST 
format ?
Cheers,

Alex Brown.