Alex,
1. MODELLER ftp services are down indeed. I apologize for that. We had some security problems, but they have been solved. Those files should be accessible again by the end of a day.
2. SEQUENCE_SEARCH can indeed take a long time. It depends on your machine's CPU and RAM. Just let it run, maybe in the evening. If it's still running next morning that something is wrong. It should finish in 2 hours or so, but then again this might be way off for your particular computer.
3. I am sure if you try google, you find them somehow.
God luck, Bozidar
> 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.