Membrane AbInitio

[Anonymous]

I was having difficulty running run_lips.pl despite instituting the suggested changes to run_lips.pl. The result was the truncated file error from alignblast.pl that everyone mentions. The suggested changes are documented in the thread below.

http://www.rosettacommons.org/content/membrane-folding-blastpgp-error#comment-4422

Both the original script and the edited run_lips.pl returned the same empty file from blastpgp. After directly entering the command generated by run_lips.pl, the result was a missing database file, nr.pin. Unfortunately, all the database files were present according to this post.

http://www.rosettacommons.org/content/membrane-folding-blastpgp-error

The reason appeared to be an old version of blastpgp contained within older versions of Rosetta. We downloaded the newest version of BLAST+, 2.2.27 from this link. Blastpgp was not located within this download. Either NCBI isn’t supporting anymore (or forgot), or we may have grabbed the wrong one.

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST

We went back to 2.2.26 and blastpgp was present. I then tried to run run_lips.pl, but I again received a truncated file. I entered the generated command into the command line and recieved absolutely nothing. I looked for instructions to the use of blastpgp and found the document below. This document and the options returned by entering blastpgp – suggested that the -d switch only specifies the type of database, not the location.

http://www.csc.fi/english/research/sciences/bioscience/programs/blast/blastpgp

I then placed all the database files,the blast suite, and the fasta and span files into one directory with run_lips.pl. With the changes to run_lips.pl listed in the first link and passing the string ‘nr’ for the database path, I was able to get a positive response from all with no errors.

There may have been some directory issues as I didn’t have permission to write in the nr database directory or the blastpgp directories. I copied everything to a directory in which I had all the available permissions. I hope this helps someone in the future.

Chris

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