I downloaded the nr database and I used the formatdb to format the database. Now I have the nr files which have been generated but I have obtained neither the nr.fasta necessary to create the filtnr by using "pfilt", nor the nrfilt files.How can I get them?
I've forwarded this to a fragments guy based on your selected category, but I haven't a clue what you're asking. I'm not sure that's a file Rosetta creates?
If you're following a set of instructions, it may be helpful to provide a link to those instructions, or mention how you obtained them.
basically, I downloaded the nr.gz database from "ftp://ftp.ncbi.nih.gov/blast/db/FASTA/", unzipped and run "formatdb -o T -i nr"..I obtained the nr files but not the nr.fasta which should be, if I understood well, necessary to run the pfilt as the rosetta 3.4 manual says (pfilt nr.fasta > filtnr). Maybe, should I add something to the formatdb command when I run that?
Are you trying to make fragments with nnmake? That's no longer recommended, except for recapitulation of previous results. The recommended way of getting fragments is to simply use the Robetta server (http://robetta.bakerlab.org/) if you're fine with the default settings, or to use the new fragment picker (http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/dc/d...) if you need to do something custom.
Note that even if you are using the new fragment picker, a copy of the vall fragment library should be included in the Rosetta 3.4 release at rosetta_database/sampling/filtered.vall.dat.2006-05-05.gz If you're really interested in making your own vall, we can get someone to explain how to do it, but in 99+% of the cases doing so isn't necessary.
First of all, the manual you are referring to is rather outdated (as it has already been pointed out). Nevertheless it is always good to have a filtered nr copy locally. In particular, you need PsiBlast locally installed to run the new fragment picker
So, fastacmd does the opposite you need: it takes nr.fasta and produces nr in its binary form ready for BLAST-ing. You need to download nr in fasta format, e.g. from here:
Run 'pfilt' on these files and after them convert them into the binary format.