Member Site › Forums › Rosetta 3 › Rosetta 3 – General › questions about ab init membrane protein
- This topic has 5 replies, 3 voices, and was last updated 13 years, 5 months ago by
htkratochvil.
-
AuthorPosts
-
-
February 7, 2011 at 9:09 am #774
Anonymous
Hello
I am trying to use the membrane ab initio modeling application by the following command:- run_lips.pl (fasta file) (span file) (path to blastpgp) (path to nr database) (path to alignblast.pl script)
example: (path to mini)/mini/src/apps/public/membrane_abinitio/run_lips.pl BRD4.fasta BRD4.span /work/bjornw/Apps/blast/bin/blastpgp /scratch/shared/genomes/nr ~bjornw/mini/src/apps/public/membrane_abinitio/alignblast.pl
But I can’t find where is (path to blastpgp) and (path to nr database), should I download these two by myself or it already includes in Rosetta3.2? could you please give me some advices for this problem?
THX
-
February 7, 2011 at 5:21 pm #4970
Anonymous
I will try to contact the membrane ab initio folks. Those programs are not really Rosetta programs but they’re part of the oldest-style fragments generating machinery. I don’t think they’re in the distribution but they may be in the fragments module.
-
February 7, 2011 at 6:26 pm #4971
Anonymous
Thank you very much.
-
February 8, 2011 at 7:39 pm #4993
Anonymous
Answers from a membrane_abinitio developer (in case others need them, I know you already got them albumns):
You need to download blast program (that contains blastpgp) and nr database (protein sequences database) at:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
Blast program and nr database also used to generate fragments – see:
http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/fragments.html
Once you install them, include full paths to their location on the command line for run_lips.pl script.
Best regards,
Vladimir -
March 16, 2011 at 8:53 pm #5187
I am also having same problem when I try to use run_lips.pl command:
readline() on closed filehandle MSA at ./run_lips.pl line 91.
I wonder if I have wrong nr database. I define the correct path for nr folder. Could you please provide a solution this problem?
-
February 14, 2011 at 7:43 pm #5020
Anonymous
I’ve got an error while I am running the following command:
/soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abi nitio/run_lips.pl test.ali test.span /usr/bin/blastp /home/albert/softbake/biosoft/rosettadb/nrdb /soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abinitio/ alignblast.pl
error:
Error in alignblast.pl: blast output file test.ali truncated:
readline() on closed filehandle MSA at /soft/rosetta-3.2/rosetta_source/src/ap ps/public/membrane_abinitio/run_lips.pl line 91.could you please tell me how to solve this?
THX
-
-
AuthorPosts
- You must be logged in to reply to this topic.