how to output a structure when scoring it?

Member Site Forums Rosetta 3 Rosetta 3 – General how to output a structure when scoring it?

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    • #1365

        Dear all,
        I use score_jd2 to score a pdb structure. But I also want to output the structure.
        I try ~/software/Rosetta_3.4/rosetta_source/bin/score_jd2.linuxgccrelease -s 1f0m.pdb -database ~/software/Rosetta_3.4/rosetta_database -out:prefix 1f0m_test -out:output
        But I didn’t get the structure. I only get the which contains the energy of the pdb.

        I think I have found the reason. I should use score instead of using score_jd2
        But the structure output by score has more H atom than original one. Is that will change the energy score? Thank you!

        Output: -nooutput don’t print PDB structures (default now)
        -output force printing of PDB structures
        -out:file:silent write silent-out file
        -out:prefix myprefix prefix the output structures with a string

      • #7518

          Have you tried -out:pdb yet?

          Where are you getting the extra H atom? Yes, having an extra atom will change the score slightly…but Rosetta won’t add it unless it thinks you need it, so there’s probably a reason for it.

        • #7523

            A small annoyance is that the flag to force PDB outputing is different between score and score_jd2 applications. The documentation is for the score application, so it lists the “-output” flag that’s used with the score application. score_jd2 (and other jd2 applications) use “-out:pdb” instead to specify PDB output.

          • #7520

              Thank you! It doesn’t change the energy score

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