I am using the score.linuxgccrelease application to score my silent file (containing 20,000 structures). I am also using the -native flag to calculate an RMS for each of these structures. (I'm trying to get an RMS vs Score plot).
I am using the command:
score_jd2.linuxgccrelease -in:file:silent P001.silent.all -out:file:silent P001.silent.all.scored -out:file:silent_struct_type binary -in:file:fullatom -database $ROSETTA_DATABASE -out:file:scorefile P001.score -native ../../master/template_master.pdb
Now, my question is: what terms in the score file relate to the RMS? In the score file, there are columns for: cen_irms and irms. But they contain different values? I can't find any documentation on what these terms are. Which is closer to a CaRMS?
Poking around the code, both are alpha carbon RMSDs. cen_irms is probably from the centroid phase of your earlier run, and irms is probably from the end of the fullatom phase. I don't know what the i stands for.
More relevantly, I'm not sure that either are being calculated by score_jd2 - are they already present in the SCORE lines in the silent file you have? I haven't tested but I get the feeling they're carryover lines from your earlier run, and the adding-RMSD function of score_jd2 (if there is one?) isn't being activated.