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 1f0m_test.sc 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
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.
Thank you! It doesn't change the energy score
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.