questions about ab init membrane protein

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    • 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
              Anonymous

                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

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