How to score the crystal structure?

[Anonymous]

Hi All,

I have a control system in which the co-crystal structure is determined. I would like to have rosetta only score the input pdb without docking, so that I can compare the crystal coordinates with the results. I would also like to be able to score the prepacked structure used for the actual studies.

I used the flag -run:score_only and this worked, but there was a score.sc file and a pdb file. Also, the rms was 30 in the score file. I re-ran and sure enough, the score was different, indicating that it is actually docking not merely scoring.

The flags I used were:
-extra_res_cen (because I have two heme proteins)
-extra_res_fa
-run:score_only
-partners A_B

then -s protein.pdb

Is there another flag I should use for scoring a structure without docking it?

Thanks

[Anonymous]

Not a different flag, but a different application. You can use the score or score_jd2 applications to get Rosetta to score any given input structure. (See http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_score_commands.html)

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