rosetta - nr database

Question

[vikisvk]

I'm trying to model the structure of a membrane protein for a final project of a university course. I'm using the following link: https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/membrane-abinitio In step 4 - generate .lips4 file I need to run:

run_lips.pl <fasta file> <span file> <path to blastpgp> <path to nr database> <path to alignblast.pl script>

I have all the required parameters except the "path to nr database", so my question is how do i get the nr database?

I've tried searching it and got to the solution of downloading a nr.gz file (21GB!) and formatting it (which is also an action that I don't fully understand how to do), is this the right way to solve this?

[GenoMax]

As the page you linked above indicates you do

need note that blastpgp and nr database are necessary to run run_lips.pl script

I am surprised that an assignment that needs a large DB does not consider its availability (I assume there are others besides you who are taking this course). Since you need to get this done, you can find pre-formatted nr blast database at this site. (You need to download all nr*.gz files and then unarchive them in a folder). It is going to be a large download.

blastpgp is no longer present in current blast+ package. Based on this post the older blast version you need to get is 2.2.26, which can be found here.

[ac.research]

Hello, thank you for your answer and the link to the database you provided.

I am currently learning how to ab initio a membrane protein and I am stuck in this same point as vikisvk, the nr database.

As you mentioned: the nr*.tar.gz database is MASSIVE (23GB), I do not have access to a fast enough internet that allows me to download this database in a reasonable amount of time.

My question is: is there a server or online tool I can use instead of having to download the database?

Any comment will help...

[GenoMax]

Since the perl script is going to run locally I don't think it would be possible to use an online resource for nr database.

Perhaps you can consider using a web server for the analysis such as ROSIE or Robetta

[ac.research]

genomax2, I meant is there a way to submit my .fasta and .span files to a web server which can calculate and return to me the .lips4 file?

I would rather run 100,000 models on an HPC and control/understand my results rather than submit a fasta sequence to a "black box server" and blindly trust what it returns to me. Do you know of such a web server?

I tried Robetta fragment generation, but it does not provide a .lips4 file.

I managed to download the 27GB nr database, and un-archive it (131GB). But running the script gave me the following error:

Error in alignblast.pl: blast output file BRD4.blast truncated: 
readline() on closed filehandle MSA at /home/computer/rosetta_src_2016.13.58602_bundle/tools/membrane_tools/run_lips.pl line 95.
Use of uninitialized value $highest_lipo_index in array element at /home/computer/rosetta_src_2016.13.58602_bundle/tools/membrane_tools/run_lips.pl line 205.

I searched online to see how to fix this error, but all the solutions I found are several years old and are not working.

Any idea what I could be doing wrong?

[WouterDeCoster]

Please use ADD COMMENT to reply to earlier comments and keep these threads easy to follow.