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.