Don’t know how to extract scores from a RNA de novo silent file.

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    • November 24, 2011 at 1:27 am #1099
      Anonymous

        Hi,

        I have a silent file containing the structures from a RNA de novo run. I have been able to extract the pdbs using the rna_extract application, but I’m unable to extract scorefiles, no matter what flags I use, it just extracts the PDB files with no scores in them. I would like to know which is the right application/flag to use, or if there’s any simple console command to get the structures in an order according to increasing total energy.

        So far I have tried:
        rna_extract.exe -out:file:scores_only -database ./rosetta_database -in:file:silent myfile.silent
        rna_extract.exe -out:file:scorefile -database ./rosetta_database -in:file:silent myfile.silent

        And a bunch of things with the score application that didn’t work.

        Thanks,
        Benjamin

      • November 24, 2011 at 1:40 am #6309
        Anonymous

          Assuming the silent file isn’t a binary type, you can probably just grep the scores right out of the file? Are there lines that start SCORE?

        • November 24, 2011 at 4:08 am #6312
          Anonymous

            Hi,

            Yes, there are lines that start with SCORE and I have typed “grep SCORE” but I just get all those lines in a messy way, what would be the proper “grep” command to print those in a *.txt file, sorted by the first column increasing value (i.e. increasing energy)?

            BTW: Does the “total score” have a defined thermodynamic meaning?

            Thanks,
            Benjamin

          • November 24, 2011 at 6:44 am #6316
            Anonymous

              Hi,

              Thanks for your advice, it worked. Now I’m trying to make structural clusters with the “cluster” application, but I get the following error:

              ERROR: unrecognized residue name ‘RCY_p:LowerRNA’
              ERROR:: Exit from: src/core/chemical/ResidueTypeSet.hh line: 151

              I’m using this flags:

              $ cluster.exe -database /rosetta/rosetta_database/ -in:file:silent wtRNA.silent -cluster:input_score_filter 0 -out:file:silent > cluster.log

              Thanks,
              Ben

            • November 25, 2011 at 8:02 pm #6330
              Anonymous

                Rhiju informs me that cluster no longer supports RNA for whatever reason. A dedicated RNA_Cluster app is slated for release in 3.4. It may be possible to use 3.2 or 3.1 for RNA clustering (?)

              • November 29, 2011 at 2:56 am #6341
                Anonymous

                  Hi,

                  So, you don’t think that what Rocco posted won’t work?
                  Sadly, I will be away from the lab for a long time now, but if you think this could work, I can show this to somebody else that might be able to try it.

                  Ben

                • November 24, 2011 at 4:11 am #6313
                  Anonymous

                    Start with “grep SCORE scorefile | sort -n -k2 > myscores.txt”. The number after k in the sort command is which column it sorts on; 2 is probably total_score. You may want to use a csv extension instead so that spreadsheet software will import it as space-delimited automatically.

                    Total_score doesn’t have a precise thermodynamic unit equivalent. It’s valid as a relative rank, the lowest score is a more plausible structure than the next lowest, but it doesn’t turn directly into kcal/mol. The scorefunction can be balanced to try to get it to resemble kcal/mol for ddGs of mutation, but that’s a long way from RNA denovo.

                  • November 25, 2011 at 1:44 am #6323
                    Anonymous

                      I would guess this is due to the cluster application looking for protein residue types, when you have RNA. For historical reasons, Rosetta doesn’t do both at once by default. There may be a document in the manual describing some mucking about with the database you can do to get RNA and protein working together; try its advice and see if it helps with this problem? I’ll bring this to the attention of a few other folks.

                    • November 25, 2011 at 6:52 pm #6328
                      Anonymous

                        There may be a document in the manual describing some mucking about with the database you can do to get RNA and protein working together;

                        http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/RNA_protein_changes.html

                        as it’s not well linked from the front page.

                      • November 27, 2011 at 12:14 am #6333
                        Anonymous

                          Rhiju corrects me; 3.1 does not work either. Sorry.

                        • November 29, 2011 at 2:11 pm #6343
                          Anonymous

                            It might, it might not – I’m not sure if anyone has tried it recently. Let us know!

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