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.
> 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 ?
ftp://ftp.rcsb.org/pub/pdb/derived_data/
-- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/
Roberto Sanchez wrote:
>>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 ? >> > >ftp://ftp.rcsb.org/pub/pdb/derived_data/ > There is also 'pdbaa':
ftp://ftp.ncbi.nih.gov/pub/blast/db/pdbaa.Z
and ASTRAL (derived from SCOP which in turn is derived from the PDB):
There are a number of very complex issues regarding the mappings between FASTA sequence files of the PDB and the actual structural data. The ASTRAL pages and literature address these issues. Caveat biologist.