questions about ab init membrane protein

Member Site Forums Rosetta 3 Rosetta 3 – General questions about ab init membrane protein

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    • #774

        I am trying to use the membrane ab initio modeling application by the following command:

 (fasta file) (span file) (path to blastpgp) (path to nr database) (path to script)

          example: (path to mini)/mini/src/apps/public/membrane_abinitio/ BRD4.fasta BRD4.span /work/bjornw/Apps/blast/bin/blastpgp /scratch/shared/genomes/nr ~bjornw/mini/src/apps/public/membrane_abinitio/

        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?


      • #4970

          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.

        • #4971

            Thank you very much.

          • #4993

              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:


              Blast program and nr database also used to generate fragments – see:


              Once you install them, include full paths to their location on the command line for script.

              Best regards,

            • #5187

                I am also having same problem when I try to use command:

                readline() on closed filehandle MSA at ./ 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?

              • #5020

                  I’ve got an error while I am running the following command:

                  /soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abi nitio/ test.ali test.span /usr/bin/blastp /home/albert/softbake/biosoft/rosettadb/nrdb /soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abinitio/

                  Error in blast output file test.ali truncated:
                  readline() on closed filehandle MSA at /soft/rosetta-3.2/rosetta_source/src/ap ps/public/membrane_abinitio/ line 91.

                  could you please tell me how to solve this?


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