question about the exposed strand results in beta_strand_homodimer_design demo

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    • #1903

        Dear developer,
        I follow the tutor to run the beta_strand_homodimer_design demo, i wanna use the method to design the EGFR dimmer,
        In order to confirm the reliable of rosetta, i download the 1IVO.pdb (Crystal structure of the complex of human epidermal growth factor and receptor ) from the PDB database and then edit the pdb file directly. I just keep one of the ERBB1 structure as the active ERBB1 receptor after deleting the others in the homodimer .
        Then i hope to predict the homodimer structure of the active ERBB1 receptor by rosetta. If everything is well, the predict beta strand homodimer results will be the
        similar with 1IVO.pdb.

        In the step of exposed strand , i could get two position for the exposed strand in the active ERBB1, paste the parts of info as follows:

        apps.public.beta_strand_homodimer_design.exposed_strand_finder: Working on: ERBB_active Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score
        core.pack.dunbrack: Dunbrack library took 0.02 seconds to load from binary
        ExposedStrand: FILE: ERBB_active CHAIN: A START: 244 END: 247 H_BONDS: 0
        ExposedStrand: FILE: ERBB_active CHAIN: A START: 253 END: 255 H_BONDS: 0
        protocols.jd2.JobDistributor: ERBB_active_0001 reported success in 2 seconds
        protocols.jd2.JobDistributor: no more batches to process…
        protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 2 seconds

        I wander how to use the above results in the second step of Make the potential homodimers,
        the make options file just give a start and a stop position for the program, I paste the demo’s make option
        file as follows:
        -run::chain A
        -sheet_start 806
        -sheet_stop 812
        -window_size 5
        -ignore_unrecognized_res true
        -mute core protocols.moves.RigidBodyMover

        can you tell me how to set the two position in the step?
        I just try to give the make option file like the following:
        -run::chain A
        -sheet_start 244
        -sheet_stop 247
        -window_size 3
        -sheet_start 253
        sheet_stop 255
        -window_size 3
        -ignore_unrecognized_res true
        -mute core protocols.moves.RigidBodyMover

        Is that right? i also attached the results here,
        It seems that the predict result is not right, for the reason is that maybe only one beta strand position have been used here.

      • #10086

          As I understand it, the homodimer_maker application will only take a single sheet that it’s going to pair up. (See the documentation That is, you’ll get a beta strand that’s exposed on one edge, and then you make a homodimer that forms by pairing up the edge of that exposed strand, so you have a continuous beta sheet across the dimer interface.

          So the sheet that you’re looking for is only going to be the single exposed strand that you’re going to match up across the interface – if you try to specify two, you’re only going to get the one strand, as the other option settings will be overwritten/ignored.

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